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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 "$foo"`
- Move publishDir before input declarations. Directives should be
before the first input. Tho this is not enforced, it may be in
future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
21 lines
529 B
Text
21 lines
529 B
Text
process samtools_index {
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tag "${bam.baseName}"
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container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
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input:
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path bam
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output:
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path "*.bai"
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script:
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def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'
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def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : ''
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"""
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samtools index $bam \\
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-@ ${task.cpus} ${avail_mem}
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samtools --version &> v_samtools.txt
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"""
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}
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