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25 lines
590 B
Text
25 lines
590 B
Text
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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(output_forward_fq), file(output_reverse_fq)
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script:
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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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