mirror of
https://github.com/MillironX/nf-core_modules.git
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5a49d2c1bf
* 📦 NEW: Add isoseq3/cluster module * 🐛FIX: Fix reports channel and add .pbi to it * 🐛FIX: Fix report channel definition * 👌IMPROVE: Move .pbi file into reports channel * 👌IMPROVE: remove --use_qvs option from command line * 👌 IMPROVE: Add in addParams removed options from command line * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: add singletons parameter and improve outputs * 🐛 FIX: Update test with last module model * 👌 IMPROVE: Add test tag * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update test data config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Remove unused index * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/cluster module * 🐛FIX: Fix reports channel and add .pbi to it * 🐛FIX: Fix report channel definition * 👌IMPROVE: Move .pbi file into reports channel * 👌IMPROVE: remove --use_qvs option from command line * 👌 IMPROVE: Add in addParams removed options from command line * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: add singletons parameter and improve outputs * 🐛 FIX: Update test with last module model * 👌 IMPROVE: Add test tag * 👌 IMPROVE: Update test data config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Remove unused index * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update code to new versions capture + better output channels * 👌 IMPROVE: Update with new versions.yml file * 🐛 FIX: Update meta.yml + correct typos * 👌 IMPROVE: Clean output file names + correct typo * 🐛 FIX: Remove bamtools/split module from isoseq3/cluster
53 lines
2.1 KiB
Text
53 lines
2.1 KiB
Text
// 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 ISOSEQ3_CLUSTER {
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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::isoseq3=3.4.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0"
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} else {
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container "quay.io/biocontainers/isoseq3:3.4.0--0"
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}
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.bam.pbi") , emit: pbi
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tuple val(meta), path("*.cluster") , emit: cluster
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tuple val(meta), path("*.cluster_report.csv"), emit: cluster_report
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tuple val(meta), path("*.transcriptset.xml") , emit: transcriptset
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tuple val(meta), path("*.hq.bam") , emit: hq_bam
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tuple val(meta), path("*.hq.bam.pbi") , emit: hq_pbi
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tuple val(meta), path("*.lq.bam") , emit: lq_bam
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tuple val(meta), path("*.lq.bam.pbi") , emit: lq_pbi
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.singletons.bam") , optional: true, emit: singletons_bam
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tuple val(meta), path("*.singletons.bam.pbi"), optional: true, emit: singletons_pbi
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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isoseq3 \\
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cluster \\
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$bam \\
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${prefix}.bam \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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isoseq3 cluster: \$( isoseq3 cluster --version|sed 's/isoseq cluster //g'|sed 's/ (.*//g' )
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END_VERSIONS
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"""
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}
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