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https://github.com/MillironX/nf-core_modules.git
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Update of pbccs (#835)
* 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: fill contains args * 👌 IMPROVE: One output => One Channel * 👌 IMPROVE: One input => One channel * 🐛 FIX: Update tests * 🐛 FIX: Remove TODOs from test.yaml * 👌 IMPROVE: Revert and keep bam and pbi together * 🐛 FIX: Remove old rq input from meta.yml * 👌 IMPROVE: Update test to match input channels * 👌 IMPROVE: use prefix for for output file name * 👌 IMPROVE: Update to new versions.yml * 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2 * 👌 IMPROVE: Keep track of the former sample id in meta * Update modules/pbccs/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * 👌 IMPROVE: remove former_id from meta * 👌 IMPROVE: Use chunk number in output filename Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Sébastien Guizard
GitHub
parent
d3369789da
commit
8524e6b40f
5 changed files with 26 additions and 29 deletions
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@ -11,11 +11,11 @@ process PBCCS {
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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::pbccs=6.0.0" : null)
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conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/pbccs:6.0.0--h9ee0642_2"
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container "https://depot.galaxyproject.org/singularity/pbccs:6.2.0--h9ee0642_0"
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} else {
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container "quay.io/biocontainers/pbccs:6.0.0--h9ee0642_2"
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container "quay.io/biocontainers/pbccs:6.2.0--h9ee0642_0"
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}
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input:
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@ -24,25 +24,22 @@ process PBCCS {
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val chunk_on
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output:
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tuple val(meta), path("*.ccs.bam") , emit: bam
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tuple val(meta), path("*.ccs.bam.pbi") , emit: pbi
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tuple val(meta), path("*.ccs_report.txt" ) , emit: ccs_report_txt
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tuple val(meta), path("*.ccs_report.json" ) , emit: ccs_report_json
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tuple val(meta), path("*.zmw_metrics.json.gz"), emit: zmw_metrics
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tuple val(meta), path("*.chunk*.bam") , emit: bam
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tuple val(meta), path("*.chunk*.bam.pbi") , emit: pbi
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tuple val(meta), path("*.report.txt" ) , emit: report_txt
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tuple val(meta), path("*.report.json" ) , emit: report_json
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tuple val(meta), path("*.metrics.json.gz"), emit: metrics
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path "versions.yml" , emit: versions
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script:
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def ccs = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs.bam'
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def report_txt = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs_report.txt'
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def report_json = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs_report.json'
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def zmw_metrics = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.zmw_metrics.json.gz'
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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ccs \\
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$bam \\
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$ccs \\
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--report-file $report_txt \\
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--report-json $report_json \\
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--metrics-json $zmw_metrics \\
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${prefix}.chunk${chunk_num}.bam \\
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--report-file ${prefix}.report.txt \\
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--report-json ${prefix}.report.json \\
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--metrics-json ${prefix}.metrics.json.gz \\
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--chunk $chunk_num/$chunk_on \\
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-j $task.cpus \\
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$options.args
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@ -16,7 +16,7 @@ input:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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id: id of the split file
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- bam:
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type: file
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description: Raw subreads bam
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BIN
tests/__pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc
Normal file
BIN
tests/__pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc
Normal file
Binary file not shown.
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@ -7,7 +7,7 @@ include { PBCCS } from '../../../modules/pbccs/main.nf' addParams( options: [arg
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workflow test_pbccs {
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input = [
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[ id:'test' ], // meta map
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[ id:'alz' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['alz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['pacbio']['alzpbi'], checkIfExists: true)
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]
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@ -3,13 +3,13 @@
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tags:
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- pbccs
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files:
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- path: output/pbccs/alz.2.ccs.bam
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md5sum: b9c8093b362a07b575d52592b19fc909
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- path: output/pbccs/alz.2.ccs.bam.pbi
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md5sum: 78d015230a8c957a24338581efda4e55
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- path: output/pbccs/alz.2.ccs_report.json
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contains: ['Created by pbcopper v1.8.0']
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- path: output/pbccs/alz.2.ccs_report.txt
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md5sum: db379e9299295679f4ca7eeb37011f08
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- path: output/pbccs/alz.2.zmw_metrics.json.gz
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contains: ['zmws']
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- path: output/pbccs/alz.chunk2.bam
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md5sum: d1a0266d5df64b74409a21981071a1c6
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- path: output/pbccs/alz.chunk2.bam.pbi
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md5sum: 582a4500ddcb3f4a24a443192620d039
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- path: output/pbccs/alz.metrics.json.gz
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contains: [ 'zmws' ]
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- path: output/pbccs/alz.report.json
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contains: [ 'Created by pbcopper' ]
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- path: output/pbccs/alz.report.txt
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md5sum: bbc5bd7a1269345cf7a7f3d4c746024b
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