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https://github.com/MillironX/nf-core_modules.git
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70daf8be30
This commit provides a minor refactoring with som
Nextflow code style improvments:
- Replaces `.toGiga()` with `.giga`
- Replaces `tag { foo }` with `tag "$foo"`
- Move publishDir before input declarations. Directives should be
before the first input. Tho this is not enforced, it may be in
future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
27 lines
704 B
Text
27 lines
704 B
Text
params.bwa_options = "-M -B 2"
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params.sequencer = "ILLUMINA"
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process bwa_mem {
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tag "$id"
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publishDir "${params.outdir}/bwa_mem", mode: 'copy'
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//TO-DO: Change container declaration, for now a test container is present in my personal docker acccount
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container 'jeremy1805/bwa-mem-img'
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input:
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tuple val(id), path(reads)
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path genomeindex
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val indexprefix
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output:
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tuple path("*.bam"), path("*.bai")
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script:
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"""
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bwa mem -t ${task.cpus} -R "@RG\\tID:${id}\\tLB:${id}\\tSM:${id}\\tPL:${params.sequencer}" \\
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${params.bwa_options} ${indexprefix} ${reads} | samtools sort -@8 -O BAM -o ${id}.bam -
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samtools index ${id}.bam
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"""
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}
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