mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 22:53:08 +00:00
remove the database auto-download for mOTUs.
This commit is contained in:
parent
53c4399052
commit
c8a59adbce
10 changed files with 53 additions and 121 deletions
54
.github/workflows/ci.yml
vendored
54
.github/workflows/ci.yml
vendored
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@ -42,8 +42,6 @@ jobs:
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- "--perform_runmerging"
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- "--perform_runmerging"
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- "--perform_runmerging --shortread_qc_mergepairs"
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- "--perform_runmerging --shortread_qc_mergepairs"
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- "--shortread_complexityfilter false --perform_shortread_hostremoval"
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- "--shortread_complexityfilter false --perform_shortread_hostremoval"
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# Test different profiles
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profile: ["test", "test_motus"]
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steps:
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steps:
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- name: Check out pipeline code
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- name: Check out pipeline code
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@ -72,4 +70,54 @@ jobs:
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# For example: adding multiple test runs with different parameters
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# For example: adding multiple test runs with different parameters
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# Remember that you can parallelise this by using strategy.matrix
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# Remember that you can parallelise this by using strategy.matrix
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run: |
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results ${{ matrix.parameters }}
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
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motus:
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name: Test mOTUs with workflow parameters
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: ${{ matrix.nxf_ver }}
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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# Nextflow versions
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include:
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# Test pipeline minimum Nextflow version
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- NXF_VER: "21.10.3"
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NXF_EDGE: ""
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# Test latest edge release of Nextflow
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- NXF_VER: ""
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NXF_EDGE: "1"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.NXF_VER }}
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# Uncomment only if the edge release is more recent than the latest stable release
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# See https://github.com/nextflow-io/nextflow/issues/2467
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# NXF_EDGE: ${{ matrix.NXF_EDGE }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Show current locale
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run: locale
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- name: Set UTF-8 enabled locale
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run: |
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sudo locale-gen en_US.UTF-8
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sudo update-locale LANG=en_US.UTF-8
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- name: Prepare the database
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run: |
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wget https://github.com/motu-tool/mOTUs/blob/master/motus/downloadDB.py
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python downloadDB.py
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echo 'tool,db_name,db_params,db_path\nmotus,db_mOTU,,db_mOTU' > 'database_motus.csv'
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- name: Run pipeline with test data
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv
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@ -353,13 +353,6 @@ process {
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]
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]
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}
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}
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withName: MOTUS_DOWNLOADDB {
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publishDir = [
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path: { "${params.outdir}/motus/db/${meta.db_name}" },
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mode: params.publish_dir_mode
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]
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}
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withName: MOTUS_PROFILE {
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withName: MOTUS_PROFILE {
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/motus/${meta.db_name}" },
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path: { "${params.outdir}/motus/${meta.db_name}" },
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@ -23,7 +23,7 @@ params {
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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databases = 'database_motus.csv'
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perform_shortread_clipmerge = false
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perform_shortread_clipmerge = false
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perform_longread_clip = false
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perform_longread_clip = false
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perform_shortread_complexityfilter = false
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perform_shortread_complexityfilter = false
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@ -138,8 +138,7 @@ Expected (uncompressed) database files for each tool are as follows:
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The database download step can be time consuming and the database will be consisting
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The database download step can be time consuming and the database will be consisting
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with same release version of the mOTUs tools. The database for same version tools
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with same release version of the mOTUs tools. The database for same version tools
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can be thus reused for multiple runs. Users can download the database once and
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can be thus reused for multiple runs. Users can download the database once and
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assign the database with the table. User can also set the parameter
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assign the database with the table.
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`download_motus_db` and let the pipeline download the database automatically.
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## Running the pipeline
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## Running the pipeline
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@ -63,9 +63,6 @@
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"minimap2/index": {
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"minimap2/index": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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},
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"motus/downloaddb": {
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"git_sha": "6393a085c5fcea11963774c041808df169907487"
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},
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"motus/profile": {
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"motus/profile": {
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"git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
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"git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
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},
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},
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39
modules/nf-core/modules/motus/downloaddb/main.nf
generated
39
modules/nf-core/modules/motus/downloaddb/main.nf
generated
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@ -1,39 +0,0 @@
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process MOTUS_DOWNLOADDB {
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label 'process_low'
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conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
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'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
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input:
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path motus_downloaddb_script
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output:
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path "db_mOTU/" , emit: db
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def software = "${motus_downloaddb_script.simpleName}_copy.py"
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"""
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## must copy script file to working directory,
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## otherwise the reference_db will be download to bin folder
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## other than current directory
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cp $motus_downloaddb_script ${software}
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python ${software} \\
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$args \\
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-t $task.cpus
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## mOTUs version number is not available from command line.
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## mOTUs save the version number in index database folder.
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## mOTUs will check the database version is same version as exec version.
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mOTUs: \$(grep motus db_mOTU/db_mOTU_versions | sed 's/motus\\t//g')
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END_VERSIONS
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"""
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}
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39
modules/nf-core/modules/motus/downloaddb/meta.yml
generated
39
modules/nf-core/modules/motus/downloaddb/meta.yml
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@ -1,39 +0,0 @@
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name: "motus_downloaddb"
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description: Download the mOTUs database
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keywords:
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- classify
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- metagenomics
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- fastq
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- taxonomic profiling
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- database
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- download
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tools:
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- "motus":
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description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data."
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homepage: "None"
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documentation: "https://github.com/motu-tool/mOTUs/wiki"
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tool_dev_url: "https://github.com/motu-tool/mOTUs"
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doi: "10.1038/s41467-019-08844-4"
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licence: "['GPL v3']"
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input:
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- motus_downloaddb:
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type: directory
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description: |
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The mOTUs downloadDB script source file.
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It is the source file installed or
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remote source in github such as https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
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pattern: "downloadDB.py"
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output:
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- db:
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type: directory
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description: The mOTUs database directory
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pattern: "db_mOTU"
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authors:
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- "@jianhong"
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@ -126,8 +126,6 @@ params {
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// mOTUs
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// mOTUs
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run_motus = false
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run_motus = false
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download_motus_db = true
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motus_downloaddb_script = 'https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'
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}
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}
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// Load base.config by default for all pipelines
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// Load base.config by default for all pipelines
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@ -430,14 +430,6 @@
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},
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},
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"run_motus": {
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"run_motus": {
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"type": "boolean"
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"type": "boolean"
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},
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"download_motus_db": {
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"type": "boolean"
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},
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"motus_downloaddb_script": {
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"type": "string",
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"default": "https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py",
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"description": "mOTUs database download script path."
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}
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}
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}
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}
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}
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}
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@ -4,7 +4,6 @@
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include { DATABASE_CHECK } from '../../modules/local/database_check'
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include { DATABASE_CHECK } from '../../modules/local/database_check'
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include { UNTAR } from '../../modules/nf-core/modules/untar/main'
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include { UNTAR } from '../../modules/nf-core/modules/untar/main'
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include { MOTUS_DOWNLOADDB } from '../../modules/nf-core/modules/motus/downloaddb/main'
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workflow DB_CHECK {
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workflow DB_CHECK {
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take:
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take:
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@ -21,22 +20,6 @@ workflow DB_CHECK {
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.splitCsv ( header:true, sep:',' )
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.splitCsv ( header:true, sep:',' )
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.map { create_db_channels(it) }
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.map { create_db_channels(it) }
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// Download database for mOTUs
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if( params.run_motus ){
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check_motus_db =
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parsed_samplesheet.filter{ it[0].tool == "motus" }
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.ifEmpty{[]}
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if( params.download_motus_db ){
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MOTUS_DOWNLOADDB( params.motus_downloaddb_script )
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check_motus_db = MOTUS_DOWNLOADDB.out.db
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.map{[
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[tool: "motus", db_name: "db_mOTU", db_params: ''],
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it
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]}
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}
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parsed_samplesheet = parsed_samplesheet.mix(check_motus_db)
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}
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ch_dbs_for_untar = parsed_samplesheet
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ch_dbs_for_untar = parsed_samplesheet
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.branch {
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.branch {
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untar: it[1].toString().endsWith(".tar.gz")
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untar: it[1].toString().endsWith(".tar.gz")
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