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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 "$foo"`
- Move publishDir before input declarations. Directives should be
before the first input. Tho this is not enforced, it may be in
future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
41 lines
1.1 KiB
Text
41 lines
1.1 KiB
Text
process cutadapt {
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tag "${sample_id}"
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container 'quay.io/biocontainers/cutadapt:1.16--py27_1'
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input:
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tuple val(sample_id), path(reads)
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output:
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tuple sample_id, path("trimmed_*.fastq")
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script:
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forward_fq = "trimmed_1.fastq"
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reverse_fq = "trimmed_2.fastq"
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if (params.single_end) {
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processing = """
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cutadapt \
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-j ${task.cpus} \
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-q $params.cutadapt_min_quality \
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--minimum-length $params.cutadapt_min_length \
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--output ${forward_fq} \
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${reads}
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"""
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} else {
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processing = """
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cutadapt \
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-j ${task.cpus} \
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-q $params.cutadapt_min_quality \
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--minimum-length $params.cutadapt_min_length \
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--pair-filter=any \
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--output ${forward_fq} \
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--paired-output ${reverse_fq} ${reads}
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"""
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}
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version = "cutadapt --version &> v_cutadapt.txt"
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return processing + version
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}
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