mirror of
https://github.com/MillironX/nf-core_modules.git
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572abb00b3
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
67 lines
2.2 KiB
Text
67 lines
2.2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = '2.2.0'
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process HISAT2_BUILD {
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tag "$fasta"
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publishDir "${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), publish_id:'') }
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conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
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} else {
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container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
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}
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input:
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path fasta
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path gtf
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path splicesites
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output:
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path "hisat2", emit: index
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path "*.version.txt", emit: version
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script:
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def avail_mem = 0
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if (!task.memory) {
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log.info "[HISAT2 index build] Available memory not known - defaulting to 0. Specify process memory requirements to change this."
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} else {
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log.info "[HISAT2 index build] Available memory: ${task.memory}"
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avail_mem = task.memory.toGiga()
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}
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def extract_exons = ''
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def ss = ''
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def exon = ''
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if (avail_mem > params.hisat_build_memory) {
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log.info "[HISAT2 index build] Over ${params.hisat_build_memory} GB available, so using splice sites and exons in HISAT2 index"
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extract_exons = "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt"
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ss = "--ss $splicesites"
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exon = "--exon ${gtf.baseName}.exons.txt"
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} else {
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log.info "[HISAT2 index build] Less than ${params.hisat_build_memory} GB available, so NOT using splice sites and exons in HISAT2 index."
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log.info "[HISAT2 index build] Use --hisat_build_memory [small number] to skip this check."
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}
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def software = getSoftwareName(task.process)
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"""
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mkdir hisat2
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$extract_exons
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hisat2-build \\
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-p $task.cpus \\
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$ss \\
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$exon \\
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$options.args \\
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$fasta \\
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hisat2/${fasta.baseName}
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echo $VERSION > ${software}.version.txt
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"""
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}
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