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27 lines
663 B
Text
27 lines
663 B
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 sample_id, file(input_forward_fq), file(input_reverse_fq)
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output:
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tuple sample_id, file(forward_fq), file(reverse_fq)
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script:
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forward_fq = "trimmed_forward.fastq"
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reverse_fq = "trimmed_reverse.fastq"
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"""
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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 ${reverse_fq} '${input_forward_fq}' '${input_reverse_fq}'
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cutadapt --version &> v_cutadapt.txt
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"""
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}
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