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https://github.com/MillironX/nf-core_modules.git
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100 lines
2.5 KiB
Text
100 lines
2.5 KiB
Text
nextflow.preview.dsl=2
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params.singlecell = ''
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params.rrbs = ''
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params.pbat = ''
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params.single_end = false
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params.trim_nextseq = 0
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params.clip_r1 = 0
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params.clip_r2 = 0
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params.three_prime_clip_r1 = 0
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params.three_prime_clip_r2 = 0
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process TRIM_GALORE {
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// container 'quay.io/biocontainers/trim-galore:0.6.5--0' // maybe later
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// tag "$sample_id"
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input:
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tuple val (name), path (reads)
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val (outdir)
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val (trim_galore_args)
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val (verbose)
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output:
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tuple val(name), path ("*fq.gz"), emit: reads
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path "*trimming_report.txt", optional: true, emit: report
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// Trimming reports are not generated for e.g. --hardtrim5, --clock etc
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// saveAs: {filename ->
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// else if (filename.indexOf("trimming_report.txt") > 0) "logs/$filename"
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// else filename
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// }
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publishDir "${outdir}/trim_galore",
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mode: "copy", overwrite: true
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script:
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if (verbose){
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println ("[MODULE] TRIM GALORE ARGS: " + trim_galore_args)
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}
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trim_galore_args += " --gzip " // we like small files
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pairedString = 0
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if (reads instanceof List) {
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pairedString = 1
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trim_galore_args += " --paired "
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}
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if (params.clip_r1 > 0){
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trim_galore_args += " --clip_r1 ${params.clip_r1} "
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}
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if (params.clip_r2 > 0){
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trim_galore_args += " --clip_r2 ${params.clip_r2} "
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}
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if (params.three_prime_clip_r1> 0){
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trim_galore_args += " --three_prime_clip_r1 ${params.three_prime_clip_r1} "
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}
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if (params.three_prime_clip_r2 > 0){
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trim_galore_args += " --three_prime_clip_r2 ${params.three_prime_clip_r2} "
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}
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if (params.trim_nextseq > 0){
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trim_galore_args += " --nextseq ${params.trim_nextseq} "
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}
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// Pre-set parameters for certain bisulfite-seq applications
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if (params.singlecell){
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trim_galore_args += " --clip_r1 6 "
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if (pairedString == 1){
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trim_galore_args += " --clip_r2 6 "
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}
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}
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if (params.rrbs){
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trim_galore_args += " --rrbs "
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}
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if (params.pbat){
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trim_galore_args += " --clip_r1 $params.pbat "
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if (pairedString == 1){
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trim_galore_args += " --clip_r2 $params.pbat "
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}
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}
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"""
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module load trim_galore
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trim_galore $trim_galore_args $reads
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"""
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}
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