mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Update all modules to new NF DSL2 syntax (#1099)
* Add comment line for consistency
* Remove all functions.nf
* Remove include functions.nf and publishDir options
* Replace options.args3 with task.ext.args3 - 3 modules
* Replace options.args3 with task.ext.args3 - 17 modules
* Replace {task.cpus} with task.cpus
* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with
* Add def args = task.ext.args line to all modules in script section
* Replace options.args with args and args_list
* Initialise args2 and args3 properly
* Replace container syntax
* Revert container changes for cellranger/mkref
* Replace getProcessName in all modules
* Replace getSoftwareName in all modules
* Unify modules using VERSION variable
* Replae options.suffix with task.ext.suffix
* Remove NF version restriction for CI
* Bump NF version in README
* Replace task.process.tokenize logic with task.process
* Minor tweaks to unify syntax in tests main.nf
* Add a separate nextflow.config for each module
* Transfer remaining module options to nextflow.config
* Remove addParams from tests main.nf
* Remove TODO statements
* Use -c to import module specific config
* Bump NF version to 21.10.3
* Fix tests for artic/minion
* Fix broken publishDir syntax
* Standardise and fix obvious failing module tests
* Remove kronatools to krona
* Comment out tags in subworkflow test.yml
* Fix failing module tests
* Add consistent indentation to nextflow.config
* Comment out subworklow definitions
* Fix kallistobustools/ref
* Fix rmarkdownnotebook
* Fix jupyternotebook
* Quote task.process
* Add plink2/vcf to pytest_modules.yml
* Remove NF_CORE_MODULES_TEST from pytest CI
* Fix more tests
* Move bacteroides_fragilis to prokaryotes folder
* Fix cooler merge tests
* Fix kallistobustools/count tests
* Fix kallistobustools/ref tests
* Update test_10x_1_fastq_gz file for kallistobustools/count tests
* Fix bcftools/query tests
* Fix delly/call tests
* Fix cooler/zoomify tests
* Fix csvtk/split tests
* Fix gatk4/intervallisttools tests
* Fix gatk4/variantfiltration
* Fix pydamage/filter tests
* Fix test data for unicycler
* Fix gstama/collapse module
* Fix leehom tests
* Fix metaphlan3 tests
* Fix pairtools/select tests
* Update nextflow.config
* Update nextflow.config
* feat: update syntax
* Fix arriba tests
* Fix more failing tests
* Update test syntax
* Remove comments from tests nextflow.config
* Apply suggestions from code review
* Fix kallistobustools/count module
* Update dumpsoftwareversions module
* Update custom/dumpsoftwareversions
* Add args2 to untar module
* Update leftover modules
* Remove last remaining addParams
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
This commit is contained in:
Harshil Patel
GitHub
parent
45985ff6f0
commit
20d8250d9f
1803 changed files with 7649 additions and 36540 deletions
4
.github/workflows/nf-core-linting.yml
vendored
4
.github/workflows/nf-core-linting.yml
vendored
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@ -7,7 +7,6 @@ on:
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pull_request:
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branches: [master]
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jobs:
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changes:
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name: Check for changes
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@ -25,9 +24,6 @@ jobs:
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lint:
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runs-on: ubuntu-20.04
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env:
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NXF_VER: 21.04.0
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name: ${{ matrix.tags }}
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needs: changes
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if: needs.changes.outputs.modules != '[]'
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10
.github/workflows/pytest-workflow.yml
vendored
10
.github/workflows/pytest-workflow.yml
vendored
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@ -23,13 +23,12 @@ jobs:
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test:
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runs-on: ubuntu-20.04
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name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
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name: ${{ matrix.tags }} ${{ matrix.profile }}
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needs: changes
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if: needs.changes.outputs.modules != '[]'
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strategy:
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fail-fast: false
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matrix:
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nxf_version: ["21.04.0"]
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tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
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profile: ["docker", "singularity", "conda"]
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env:
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@ -60,13 +59,12 @@ jobs:
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- uses: actions/cache@v2
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with:
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path: /usr/local/bin/nextflow
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key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
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key: ${{ runner.os }}
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restore-keys: |
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${{ runner.os }}-nextflow-
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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CAPSULE_LOG: none
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run: |
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wget -qO- get.nextflow.io | bash
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@ -93,13 +91,13 @@ jobs:
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# Test the module
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- name: Run pytest-workflow
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# only use one thread for pytest-workflow to avoid race condition on conda cache.
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run: NF_CORE_MODULES_TEST=1 TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
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run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
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- name: Upload logs on failure
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if: failure()
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uses: actions/upload-artifact@v2
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with:
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name: logs-${{ matrix.profile }}-${{ matrix.nxf_version }}
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name: logs-${{ matrix.profile }}
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path: |
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/home/runner/pytest_workflow_*/*/.nextflow.log
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/home/runner/pytest_workflow_*/*/log.out
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@ -1,6 +1,6 @@
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# 
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[](https://www.nextflow.io/)
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[](https://www.nextflow.io/)
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[](https://docs.conda.io/en/latest/)
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[](https://www.docker.com/)
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[](https://sylabs.io/docs/)
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@ -78,7 +78,7 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
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nextflow.enable.dsl = 2
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include { FASTQC } from './modules/nf-core/modules/fastqc/main' addParams( options: [:] )
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include { FASTQC } from './modules/nf-core/modules/fastqc/main'
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```
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5. Remove the module from the pipeline repository if required:
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@ -1,78 +0,0 @@
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//
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// Utility functions used in nf-core DSL2 module files
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//
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//
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// Extract name of software tool from process name using $task.process
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//
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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//
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// Extract name of module from process name using $task.process
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//
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def getProcessName(task_process) {
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return task_process.tokenize(':')[-1]
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}
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//
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// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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//
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_meta = args.publish_by_meta ?: []
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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//
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// Tidy up and join elements of a list to return a path string
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//
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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//
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// Function to save/publish module results
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//
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def saveFiles(Map args) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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// Do not publish versions.yml unless running from pytest workflow
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if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
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return null
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}
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if (ioptions.publish_by_meta) {
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def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
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for (key in key_list) {
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if (args.meta && key instanceof String) {
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def path = key
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if (args.meta.containsKey(key)) {
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path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
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}
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path = path instanceof String ? path : ''
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path_list.add(path)
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}
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}
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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@ -1,22 +1,11 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process ABACAS {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0"
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} else {
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container "quay.io/biocontainers/abacas:1.3.1--pl526_0"
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}
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' :
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'quay.io/biocontainers/abacas:1.3.1--pl526_0' }"
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input:
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tuple val(meta), path(scaffold)
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@ -27,12 +16,13 @@ process ABACAS {
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def args = task.ext.args ?: ''
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def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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"""
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abacas.pl \\
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-r $fasta \\
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-q $scaffold \\
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$options.args \\
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$args \\
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-o ${prefix}.abacas
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mv nucmer.delta ${prefix}.abacas.nucmer.delta
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@ -40,8 +30,8 @@ process ABACAS {
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mv nucmer.tiling ${prefix}.abacas.nucmer.tiling
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mv unused_contigs.out ${prefix}.abacas.unused.contigs.out
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//')
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"${task.process}":
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abacas: \$(echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -1,78 +0,0 @@
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//
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// Utility functions used in nf-core DSL2 module files
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//
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//
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// Extract name of software tool from process name using $task.process
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//
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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//
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// Extract name of module from process name using $task.process
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//
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def getProcessName(task_process) {
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return task_process.tokenize(':')[-1]
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}
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//
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// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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//
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_meta = args.publish_by_meta ?: []
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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//
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// Tidy up and join elements of a list to return a path string
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//
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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//
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// Function to save/publish module results
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//
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def saveFiles(Map args) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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// Do not publish versions.yml unless running from pytest workflow
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if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
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return null
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}
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if (ioptions.publish_by_meta) {
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def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
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for (key in key_list) {
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if (args.meta && key instanceof String) {
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def path = key
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if (args.meta.containsKey(key)) {
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path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
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}
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path = path instanceof String ? path : ''
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path_list.add(path)
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}
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}
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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@ -1,21 +1,11 @@
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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||||
|
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params.options = [:]
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options = initOptions(params.options)
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|
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process ADAPTERREMOVAL {
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tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
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mode: params.publish_dir_mode,
|
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0"
|
||||
} else {
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container "quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
|
||||
'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"
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||||
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||||
input:
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||||
tuple val(meta), path(reads)
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@ -26,13 +16,14 @@ process ADAPTERREMOVAL {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
AdapterRemoval \\
|
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--file1 $reads \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--basename $prefix \\
|
||||
--threads $task.cpus \\
|
||||
--settings ${prefix}.log \\
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||||
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@ -41,8 +32,8 @@ process ADAPTERREMOVAL {
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--gzip \\
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
||||
"${task.process}":
|
||||
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else if (!meta.single_end && !meta.collapse) {
|
||||
|
|
@ -50,7 +41,7 @@ process ADAPTERREMOVAL {
|
|||
AdapterRemoval \\
|
||||
--file1 ${reads[0]} \\
|
||||
--file2 ${reads[1]} \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--basename $prefix \\
|
||||
--threads $task.cpus \\
|
||||
--settings ${prefix}.log \\
|
||||
|
|
@ -60,8 +51,8 @@ process ADAPTERREMOVAL {
|
|||
--gzip \\
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
||||
"${task.process}":
|
||||
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
|
|
@ -70,7 +61,7 @@ process ADAPTERREMOVAL {
|
|||
--file1 ${reads[0]} \\
|
||||
--file2 ${reads[1]} \\
|
||||
--collapse \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--basename $prefix \\
|
||||
--threads $task.cpus \\
|
||||
--settings ${prefix}.log \\
|
||||
|
|
@ -79,8 +70,8 @@ process ADAPTERREMOVAL {
|
|||
|
||||
cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
||||
"${task.process}":
|
||||
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process AGRVATE {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/agrvate:1.0.2--hdfd78af_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/agrvate:1.0.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
|
@ -27,15 +16,16 @@ process AGRVATE {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
agrvate \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
-i $fasta
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(echo \$(agrvate -v 2>&1) | sed 's/agrvate v//;')
|
||||
"${task.process}":
|
||||
agrvate: \$(echo \$(agrvate -v 2>&1) | sed 's/agrvate v//;')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process ALLELECOUNTER {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' :
|
||||
'quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index)
|
||||
|
|
@ -28,20 +17,21 @@ process ALLELECOUNTER {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def reference_options = fasta ? "-r $fasta": ""
|
||||
|
||||
"""
|
||||
alleleCounter \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
-l $loci \\
|
||||
-b $input \\
|
||||
$reference_options \\
|
||||
-o ${prefix}.alleleCount
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(alleleCounter --version)
|
||||
"${task.process}":
|
||||
allelecounter: \$(alleleCounter --version)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,21 +1,10 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process AMPS {
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hops=0.35" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1"
|
||||
} else {
|
||||
container "quay.io/biocontainers/hops:0.35--hdfd78af_1"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' :
|
||||
'quay.io/biocontainers/hops:0.35--hdfd78af_1' }"
|
||||
|
||||
input:
|
||||
path maltextract_results
|
||||
|
|
@ -30,6 +19,7 @@ process AMPS {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
postprocessing.AMPS.r \\
|
||||
-r $maltextract_results \\
|
||||
|
|
@ -37,11 +27,11 @@ process AMPS {
|
|||
-m $filter \\
|
||||
-t $task.cpus \\
|
||||
-j \\
|
||||
$options.args
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
|
||||
"${task.process}":
|
||||
amps: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process ARRIBA {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::arriba=2.1.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1"
|
||||
} else {
|
||||
container "quay.io/biocontainers/arriba:2.1.0--h3198e80_1"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1' :
|
||||
'quay.io/biocontainers/arriba:2.1.0--h3198e80_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
@ -29,8 +18,9 @@ process ARRIBA {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def blacklist = (options.args.contains('-b')) ? '' : '-f blacklist'
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def blacklist = (args.contains('-b')) ? '' : '-f blacklist'
|
||||
"""
|
||||
arriba \\
|
||||
-x $bam \\
|
||||
|
|
@ -39,11 +29,11 @@ process ARRIBA {
|
|||
-o ${prefix}.fusions.tsv \\
|
||||
-O ${prefix}.fusions.discarded.tsv \\
|
||||
$blacklist \\
|
||||
$options.args
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s//')
|
||||
"${task.process}":
|
||||
arriba: \$(arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process ARTIC_GUPPYPLEX {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::artic=1.2.1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/artic:1.2.1--py_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0' :
|
||||
'quay.io/biocontainers/artic:1.2.1--py_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fastq_dir)
|
||||
|
|
@ -26,18 +15,19 @@ process ARTIC_GUPPYPLEX {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
artic \\
|
||||
guppyplex \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--directory $fastq_dir \\
|
||||
--output ${prefix}.fastq
|
||||
|
||||
pigz -p $task.cpus *.fastq
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
artic: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process ARTIC_MINION {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::artic=1.2.1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/artic:1.2.1--py_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0' :
|
||||
'quay.io/biocontainers/artic:1.2.1--py_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fastq)
|
||||
|
|
@ -43,20 +32,21 @@ process ARTIC_MINION {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def version = scheme_version.toString().toLowerCase().replaceAll('v','')
|
||||
def fast5 = params.fast5_dir ? "--fast5-directory $fast5_dir" : ""
|
||||
def summary = params.sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""
|
||||
def fast5 = fast5_dir ? "--fast5-directory $fast5_dir" : ""
|
||||
def summary = sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""
|
||||
def model = ""
|
||||
if (options.args.tokenize().contains('--medaka')) {
|
||||
if (args.tokenize().contains('--medaka')) {
|
||||
fast5 = ""
|
||||
summary = ""
|
||||
model = file(params.artic_minion_medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $params.artic_minion_medaka_model"
|
||||
model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
|
||||
}
|
||||
"""
|
||||
artic \\
|
||||
minion \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--threads $task.cpus \\
|
||||
--read-file $fastq \\
|
||||
--scheme-directory ./primer-schemes \\
|
||||
|
|
@ -68,8 +58,8 @@ process ARTIC_MINION {
|
|||
$prefix
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
artic: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process ASSEMBLYSCAN {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/assembly-scan:0.4.1--pyhdfd78af_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/assembly-scan:0.4.1--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(assembly)
|
||||
|
|
@ -26,13 +15,14 @@ process ASSEMBLYSCAN {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
assembly-scan $assembly > ${prefix}.json
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$( assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\$//' )
|
||||
"${task.process}":
|
||||
assemblyscan: \$( assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\$//' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,21 +1,11 @@
|
|||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process ATAQV_ATAQV {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::ataqv=1.2.1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2"
|
||||
} else {
|
||||
container "quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2' :
|
||||
'quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai), path(peak_file)
|
||||
|
|
@ -30,14 +20,15 @@ process ATAQV_ATAQV {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def peak = peak_file ? "--peak-file $peak_file" : ''
|
||||
def tss = tss_file ? "--tss-file $tss_file" : ''
|
||||
def excl_regs = excl_regs_file ? "--excluded-region-file $excl_regs_file" : ''
|
||||
def autosom_ref = autosom_ref_file ? "--autosomal-reference-file $autosom_ref_file" : ''
|
||||
"""
|
||||
ataqv \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
$peak \\
|
||||
$tss \\
|
||||
$excl_regs \\
|
||||
|
|
@ -49,8 +40,8 @@ process ATAQV_ATAQV {
|
|||
$bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$( ataqv --version )
|
||||
"${task.process}":
|
||||
ataqv: \$( ataqv --version )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BAKTA {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bakta=1.2.2" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
|
@ -37,27 +26,28 @@ process BAKTA {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
|
||||
def prodigal_opt = prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : ""
|
||||
"""
|
||||
bakta \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--threads $task.cpus \\
|
||||
--prefix ${prefix} \\
|
||||
--prefix $prefix \\
|
||||
--db $db \\
|
||||
$proteins_opt \\
|
||||
$prodigal_tf \\
|
||||
$fasta
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
|
||||
"${task.process}":
|
||||
bakta: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
|
||||
stub:
|
||||
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
touch ${prefix}.embl
|
||||
touch ${prefix}.faa
|
||||
|
|
@ -70,8 +60,8 @@ process BAKTA {
|
|||
touch ${prefix}.tsv
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
|
||||
"${task.process}":
|
||||
bakta: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BAMALIGNCLEANER {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bamaligncleaner:0.2.1--pyhdfd78af_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/bamaligncleaner:0.2.1--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
@ -26,17 +15,18 @@ process BAMALIGNCLEANER {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
|
||||
"""
|
||||
bamAlignCleaner \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
-o ${prefix}.bam \\
|
||||
${bam}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bamAlignCleaner --version | sed 's/.*version //')
|
||||
"${task.process}":
|
||||
bamaligncleaner: \$(bamAlignCleaner --version | sed 's/.*version //')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BAMTOOLS_SPLIT {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bamtools:2.5.1--h9a82719_9"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
|
||||
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
@ -26,16 +15,17 @@ process BAMTOOLS_SPLIT {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bamtools \\
|
||||
split \\
|
||||
-in $bam \\
|
||||
$options.args
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
|
||||
"${task.process}":
|
||||
bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BAMUTIL_TRIMBAM {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bamutil:1.0.15--h2e03b76_1"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1' :
|
||||
'quay.io/biocontainers/bamutil:1.0.15--h2e03b76_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), val(trim_left), val(trim_right)
|
||||
|
|
@ -26,19 +15,20 @@ process BAMUTIL_TRIMBAM {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bam \\
|
||||
trimBam \\
|
||||
$bam \\
|
||||
${prefix}.bam \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
-L $trim_left \\
|
||||
-R $trim_right
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$( echo \$( bam trimBam 2>&1 ) | sed 's/^Version: //;s/;.*//' )
|
||||
"${task.process}":
|
||||
bamutil: \$( echo \$( bam trimBam 2>&1 ) | sed 's/^Version: //;s/;.*//' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BANDAGE_IMAGE {
|
||||
tag "${meta.id}"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bandage:0.8.1--hc9558a2_2"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2' :
|
||||
'quay.io/biocontainers/bandage:0.8.1--hc9558a2_2' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(gfa)
|
||||
|
|
@ -27,14 +16,15 @@ process BANDAGE_IMAGE {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
Bandage image $gfa ${prefix}.png $options.args
|
||||
Bandage image $gfa ${prefix}.svg $options.args
|
||||
Bandage image $gfa ${prefix}.png $args
|
||||
Bandage image $gfa ${prefix}.svg $args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bandage: \$(echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BBMAP_ALIGN {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
|
||||
'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fastq)
|
||||
|
|
@ -28,7 +17,8 @@ process BBMAP_ALIGN {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
|
||||
input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}"
|
||||
|
||||
|
|
@ -50,14 +40,14 @@ process BBMAP_ALIGN {
|
|||
$db \\
|
||||
$input \\
|
||||
out=${prefix}.bam \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
threads=$task.cpus \\
|
||||
-Xmx${task.memory.toGiga()}g \\
|
||||
&> ${prefix}.bbmap.log
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bbversion.sh)
|
||||
"${task.process}":
|
||||
bbmap: \$(bbversion.sh)
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
|
||||
END_VERSIONS
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,21 +1,11 @@
|
|||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BBMAP_BBDUK {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bbmap=38.90" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bbmap:38.90--he522d1c_1"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' :
|
||||
'quay.io/biocontainers/bbmap:38.90--he522d1c_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
@ -27,7 +17,8 @@ process BBMAP_BBDUK {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}"
|
||||
def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
|
||||
def contaminants_fa = contaminants ? "ref=$contaminants" : ''
|
||||
|
|
@ -38,12 +29,12 @@ process BBMAP_BBDUK {
|
|||
$raw \\
|
||||
$trimmed \\
|
||||
threads=$task.cpus \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
$contaminants_fa \\
|
||||
&> ${prefix}.bbduk.log
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bbversion.sh)
|
||||
"${task.process}":
|
||||
bbmap: \$(bbversion.sh)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,21 +1,10 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BBMAP_BBSPLIT {
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bbmap=38.93" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bbmap:38.93--he522d1c_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0' :
|
||||
'quay.io/biocontainers/bbmap:38.93--he522d1c_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
@ -32,7 +21,8 @@ process BBMAP_BBSPLIT {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
|
|
@ -54,11 +44,11 @@ process BBMAP_BBSPLIT {
|
|||
${other_refs.join(' ')} \\
|
||||
path=bbsplit \\
|
||||
threads=$task.cpus \\
|
||||
$options.args
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bbversion.sh 2>&1)
|
||||
"${task.process}":
|
||||
bbmap: \$(bbversion.sh 2>&1)
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
|
|
@ -83,11 +73,11 @@ process BBMAP_BBSPLIT {
|
|||
$fastq_in \\
|
||||
$fastq_out \\
|
||||
refstats=${prefix}.stats.txt \\
|
||||
$options.args
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bbversion.sh 2>&1)
|
||||
"${task.process}":
|
||||
bbmap: \$(bbversion.sh 2>&1)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BBMAP_INDEX {
|
||||
tag "$fasta"
|
||||
label 'process_long'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bbmap=38.92" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bbmap:38.92--he522d1c_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0' :
|
||||
'quay.io/biocontainers/bbmap:38.92--he522d1c_0' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
|
|
@ -26,16 +15,17 @@ process BBMAP_INDEX {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
bbmap.sh \\
|
||||
ref=${fasta} \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
threads=$task.cpus \\
|
||||
-Xmx${task.memory.toGiga()}g
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bbversion.sh)
|
||||
"${task.process}":
|
||||
bbmap: \$(bbversion.sh)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_CONCAT {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0' :
|
||||
'quay.io/biocontainers/bcftools:1.11--h7c999a4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcfs)
|
||||
|
|
@ -26,17 +15,18 @@ process BCFTOOLS_CONCAT {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bcftools concat \\
|
||||
--output ${prefix}.vcf.gz \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--threads $task.cpus \\
|
||||
${vcfs}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_CONSENSUS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container 'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0'
|
||||
} else {
|
||||
container 'quay.io/biocontainers/bcftools:1.13--h3a49de5_0'
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(fasta)
|
||||
|
|
@ -26,15 +15,16 @@ process BCFTOOLS_CONSENSUS {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
cat $fasta | bcftools consensus $vcf $options.args > ${prefix}.fa
|
||||
cat $fasta | bcftools consensus $vcf $args > ${prefix}.fa
|
||||
header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
|
||||
sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_FILTER {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
@ -26,16 +15,17 @@ process BCFTOOLS_FILTER {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bcftools filter \\
|
||||
--output ${prefix}.vcf.gz \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
$vcf
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_INDEX {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
@ -27,18 +16,19 @@ process BCFTOOLS_INDEX {
|
|||
path "versions.yml" , emit: version
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
|
||||
"""
|
||||
bcftools \\
|
||||
index \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--threads $task.cpus \\
|
||||
$vcf
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_ISEC {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcfs), path(tbis)
|
||||
|
|
@ -26,15 +15,16 @@ process BCFTOOLS_ISEC {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bcftools isec \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
-p $prefix \\
|
||||
*.vcf.gz
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_MERGE {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcfs), path(tbis)
|
||||
|
|
@ -26,15 +15,16 @@ process BCFTOOLS_MERGE {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bcftools merge -Oz \\
|
||||
--output ${prefix}.vcf.gz \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
*.vcf.gz
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_MPILEUP {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
@ -29,21 +18,28 @@ process BCFTOOLS_MPILEUP {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def args2 = task.ext.args2 ?: ''
|
||||
def args3 = task.ext.args3 ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
echo "${meta.id}" > sample_name.list
|
||||
|
||||
bcftools mpileup \\
|
||||
--fasta-ref $fasta \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
$bam \\
|
||||
| bcftools call --output-type v $options.args2 \\
|
||||
| bcftools call --output-type v $args2 \\
|
||||
| bcftools reheader --samples sample_name.list \\
|
||||
| bcftools view --output-file ${prefix}.vcf.gz --output-type z $options.args3
|
||||
| bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3
|
||||
|
||||
tabix -p vcf -f ${prefix}.vcf.gz
|
||||
|
||||
bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_NORM {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
@ -27,18 +16,19 @@ process BCFTOOLS_NORM {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bcftools norm \\
|
||||
--fasta-ref ${fasta} \\
|
||||
--output ${prefix}.vcf.gz \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--threads $task.cpus \\
|
||||
${vcf}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_QUERY {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(index)
|
||||
|
|
@ -29,7 +18,8 @@ process BCFTOOLS_QUERY {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def regions_file = regions ? "--regions-file ${regions}" : ""
|
||||
def targets_file = targets ? "--targets-file ${targets}" : ""
|
||||
def samples_file = samples ? "--samples-file ${samples}" : ""
|
||||
|
|
@ -40,12 +30,12 @@ process BCFTOOLS_QUERY {
|
|||
${regions_file} \\
|
||||
${targets_file} \\
|
||||
${samples_file} \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
${vcf}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_REHEADER {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
@ -28,7 +17,8 @@ process BCFTOOLS_REHEADER {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def update_sequences = fai ? "-f $fai" : ""
|
||||
def new_header = header ? "-h $header" : ""
|
||||
"""
|
||||
|
|
@ -36,14 +26,14 @@ process BCFTOOLS_REHEADER {
|
|||
reheader \\
|
||||
$update_sequences \\
|
||||
$new_header \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--threads $task.cpus \\
|
||||
-o ${prefix}.vcf.gz \\
|
||||
$vcf
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_STATS {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
@ -26,12 +15,13 @@ process BCFTOOLS_STATS {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bcftools stats $options.args $vcf > ${prefix}.bcftools_stats.txt
|
||||
bcftools stats $args $vcf > ${prefix}.bcftools_stats.txt
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BCFTOOLS_VIEW {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(index)
|
||||
|
|
@ -29,25 +18,24 @@ process BCFTOOLS_VIEW {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def regions_file = regions ? "--regions-file ${regions}" : ""
|
||||
def targets_file = targets ? "--targets-file ${targets}" : ""
|
||||
def samples_file = samples ? "--samples-file ${samples}" : ""
|
||||
|
||||
|
||||
"""
|
||||
bcftools view \\
|
||||
--output ${prefix}.vcf.gz \\
|
||||
${regions_file} \\
|
||||
${targets_file} \\
|
||||
${samples_file} \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--threads $task.cpus \\
|
||||
${vcf}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_BAMTOBED {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
@ -26,17 +15,18 @@ process BEDTOOLS_BAMTOBED {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
bamtobed \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
-i $bam \\
|
||||
| bedtools sort > ${prefix}.bed
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_COMPLEMENT {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
|
|
@ -27,18 +16,19 @@ process BEDTOOLS_COMPLEMENT {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
complement \\
|
||||
-i $bed \\
|
||||
-g $sizes \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
> ${prefix}.bed
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_GENOMECOV {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals), val(scale)
|
||||
|
|
@ -28,15 +17,14 @@ process BEDTOOLS_GENOMECOV {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args_token = options.args.tokenize()
|
||||
def args = options.args
|
||||
def args = task.ext.args ?: ''
|
||||
def args_list = args.tokenize()
|
||||
args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
|
||||
|
||||
if (!args_token.contains('-bg') && (scale > 0 && scale != 1)) {
|
||||
if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) {
|
||||
args += " -bg"
|
||||
}
|
||||
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
if (intervals.name =~ /\.bam/) {
|
||||
"""
|
||||
bedtools \\
|
||||
|
|
@ -46,8 +34,8 @@ process BEDTOOLS_GENOMECOV {
|
|||
> ${prefix}.${extension}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
|
|
@ -60,8 +48,8 @@ process BEDTOOLS_GENOMECOV {
|
|||
> ${prefix}.${extension}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_GETFASTA {
|
||||
tag "$bed"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
||||
|
||||
input:
|
||||
path bed
|
||||
|
|
@ -27,18 +16,19 @@ process BEDTOOLS_GETFASTA {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${bed.baseName}${options.suffix}" : "${bed.baseName}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${bed.baseName}${task.ext.suffix}" : "${bed.baseName}"
|
||||
"""
|
||||
bedtools \\
|
||||
getfasta \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
-fi $fasta \\
|
||||
-bed $bed \\
|
||||
-fo ${prefix}.fa
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_INTERSECT {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals1), path(intervals2)
|
||||
|
|
@ -27,18 +16,19 @@ process BEDTOOLS_INTERSECT {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
intersect \\
|
||||
-a $intervals1 \\
|
||||
-b $intervals2 \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
> ${prefix}.${extension}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_MAKEWINDOWS {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(regions)
|
||||
|
|
@ -27,18 +16,19 @@ process BEDTOOLS_MAKEWINDOWS {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def arg_input = use_bed ? "-b $regions" : "-g $regions"
|
||||
"""
|
||||
bedtools \\
|
||||
makewindows \\
|
||||
${arg_input} \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
> ${prefix}.tab
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_MASKFASTA {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
|
|
@ -27,17 +16,18 @@ process BEDTOOLS_MASKFASTA {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
maskfasta \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
-fi $fasta \\
|
||||
-bed $bed \\
|
||||
-fo ${prefix}.fa
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_MERGE {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
|
|
@ -26,17 +15,18 @@ process BEDTOOLS_MERGE {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
merge \\
|
||||
-i $bed \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
> ${prefix}.bed
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_SLOP {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
|
|
@ -27,18 +16,19 @@ process BEDTOOLS_SLOP {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
slop \\
|
||||
-i $bed \\
|
||||
-g $sizes \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
> ${prefix}.bed
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_SORT {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals)
|
||||
|
|
@ -27,17 +16,18 @@ process BEDTOOLS_SORT {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
sort \\
|
||||
-i $intervals \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
> ${prefix}.${extension}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BEDTOOLS_SUBTRACT {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
|
||||
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals1), path(intervals2)
|
||||
|
|
@ -26,18 +15,19 @@ process BEDTOOLS_SUBTRACT {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedtools \\
|
||||
subtract \\
|
||||
-a $intervals1 \\
|
||||
-b $intervals2 \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
> ${prefix}.bed
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BISMARK_ALIGN {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bismark:0.23.0--0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
|
||||
'quay.io/biocontainers/bismark:0.23.0--0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
@ -29,18 +18,19 @@ process BISMARK_ALIGN {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def fastq = meta.single_end ? reads : "-1 ${reads[0]} -2 ${reads[1]}"
|
||||
"""
|
||||
bismark \\
|
||||
$fastq \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
--genome $index \\
|
||||
--bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
"${task.process}":
|
||||
bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BISMARK_DEDUPLICATE {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bismark:0.23.0--0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
|
||||
'quay.io/biocontainers/bismark:0.23.0--0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
@ -27,17 +16,18 @@ process BISMARK_DEDUPLICATE {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
def seqtype = meta.single_end ? '-s' : '-p'
|
||||
"""
|
||||
deduplicate_bismark \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
$seqtype \\
|
||||
--bam $bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
"${task.process}":
|
||||
bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BISMARK_GENOMEPREPARATION {
|
||||
tag "$fasta"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bismark:0.23.0--0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
|
||||
'quay.io/biocontainers/bismark:0.23.0--0' }"
|
||||
|
||||
input:
|
||||
path fasta, stageAs: "BismarkIndex/*"
|
||||
|
|
@ -26,14 +15,15 @@ process BISMARK_GENOMEPREPARATION {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
bismark_genome_preparation \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
BismarkIndex
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
"${task.process}":
|
||||
bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BISMARK_METHYLATIONEXTRACTOR {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bismark:0.23.0--0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
|
||||
'quay.io/biocontainers/bismark:0.23.0--0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
@ -31,6 +20,7 @@ process BISMARK_METHYLATIONEXTRACTOR {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def seqtype = meta.single_end ? '-s' : '-p'
|
||||
"""
|
||||
bismark_methylation_extractor \\
|
||||
|
|
@ -39,12 +29,12 @@ process BISMARK_METHYLATIONEXTRACTOR {
|
|||
--gzip \\
|
||||
--report \\
|
||||
$seqtype \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
$bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
"${task.process}":
|
||||
bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BISMARK_REPORT {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bismark:0.23.0--0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
|
||||
'quay.io/biocontainers/bismark:0.23.0--0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias)
|
||||
|
|
@ -26,12 +15,13 @@ process BISMARK_REPORT {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
bismark2report $options.args
|
||||
bismark2report $args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
"${task.process}":
|
||||
bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,21 +1,10 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||||
|
||||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
process BISMARK_SUMMARY {
|
||||
label 'process_low'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bismark:0.23.0--0"
|
||||
}
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
|
||||
'quay.io/biocontainers/bismark:0.23.0--0' }"
|
||||
|
||||
input:
|
||||
path(bam)
|
||||
|
|
@ -29,12 +18,13 @@ process BISMARK_SUMMARY {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
bismark2summary
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
"${task.process}":
|
||||
bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,78 +0,0 @@
|
|||
//
|
||||
// Utility functions used in nf-core DSL2 module files
|
||||
//
|
||||
|
||||
//
|
||||
// Extract name of software tool from process name using $task.process
|
||||
//
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
//
|
||||
// Extract name of module from process name using $task.process
|
||||
//
|
||||
def getProcessName(task_process) {
|
||||
return task_process.tokenize(':')[-1]
|
||||
}
|
||||
|
||||
//
|
||||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
//
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.args3 = args.args3 ?: ''
|
||||
options.publish_by_meta = args.publish_by_meta ?: []
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
//
|
||||
// Tidy up and join elements of a list to return a path string
|
||||
//
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
//
|
||||
// Function to save/publish module results
|
||||
//
|
||||
def saveFiles(Map args) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
|
||||
// Do not publish versions.yml unless running from pytest workflow
|
||||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
|
||||
return null
|
||||
}
|
||||
if (ioptions.publish_by_meta) {
|
||||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
|
||||
for (key in key_list) {
|
||||
if (args.meta && key instanceof String) {
|
||||
def path = key
|
||||
if (args.meta.containsKey(key)) {
|
||||
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
|
||||
}
|
||||
path = path instanceof String ? path : ''
|
||||
path_list.add(path)
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else if (ioptions.publish_files == null) {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
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