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35 lines
1.1 KiB
Text
35 lines
1.1 KiB
Text
process fastqc {
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tag "$sample_id"
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publishDir "${params.outdir}/trim_galore", mode: 'copy',
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saveAs: {filename ->
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if (filename.indexOf("_fastqc") > 0) "FastQC/$filename"
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else if (filename.indexOf("trimming_report.txt") > 0) "logs/$filename"
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else filename
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}
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container: 'quay.io/biocontainers/trim-galore:0.6.5--0'
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input:
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set val(sample_id), file(reads)
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output:
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set val(name), file("*fq.gz")
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file "*trimming_report.txt"
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file "*_fastqc.{zip,html}"
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script:
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c_r1 = clip_r1 > 0 ? "--clip_r1 ${clip_r1}" : ''
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c_r2 = clip_r2 > 0 ? "--clip_r2 ${clip_r2}" : ''
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tpc_r1 = three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${three_prime_clip_r1}" : ''
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tpc_r2 = three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${three_prime_clip_r2}" : ''
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nextseq = params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : ''
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if (params.singleEnd) {
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"""
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trim_galore --fastqc --gzip $c_r1 $tpc_r1 $nextseq $reads
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"""
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} else {
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"""
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trim_galore --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq $reads
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"""
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}
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}
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