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Verified Commit 5af36606 authored by Laurent Modolo's avatar Laurent Modolo
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cutadapt: update to last contributing guide version

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src/nf_modules/cutadapt/main.nf
+ 36
− 101
View file @ 5af36606
version = "2.1" version = "2.1"
container_url = "lbmc/cutadapt:${version}" container_url = "lbmc/cutadapt:${version}"
adapter_3_prim = "AGATCGGAAGAG" params.adapter_3_prim = "AGATCGGAAGAG"
adapter_5_prim = "CTCTTCCGATCT" params.adapter_5_prim = "CTCTTCCGATCT"
trim_quality = "20" params.adaptor_removal = "-a ${params.adapter_3_prim} -g ${params.adapter_5_prim} -A ${params.adapter_3_prim} -G ${params.adapter_5_prim}"
params.adaptor_removal_out = ""
params.adaptor_removal = "-a ${adapter_3_prim} -g ${adapter_5_prim} -A ${adapter_3_prim} -G ${adapter_5_prim}"
process adaptor_removal { process adaptor_removal {
container = "${container_url}" container = "${container_url}"
label "big_mem_mono_cpus" label "big_mem_mono_cpus"
tag "$pair_id" tag "$file_id"
if (params.adaptor_removal_out != "") {
publishDir "results/${params.adaptor_removal_out}", mode: 'copy'
}
input: input:
tuple val(pair_id), path(reads) tuple val(file_id), path(reads)
output: output:
tuple val(pair_id), path("*_cut_R{1,2}.fastq.gz"), emit: fastq tuple val(file_id), path("*_cut_R{1,2}.fastq.gz"), emit: fastq
path "*_report.txt", emit: report path "*_report.txt", emit: report
script: script:
if (reads instanceof List) if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
if (reads.size() == 2)
""" """
cutadapt ${params.adaptor_removal} \ cutadapt ${params.adaptor_removal} \
-o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \ -o ${file_id}_cut_R1.fastq.gz -p ${file_id}_cut_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt ${reads[0]} ${reads[1]} > ${file_id}_report.txt
""" """
else else
""" """
...@@ -33,112 +40,40 @@ process adaptor_removal { ...@@ -33,112 +40,40 @@ process adaptor_removal {
""" """
} }
params.adaptor_removal_pairedend = "-a ${adapter_3_prim} -g ${adapter_5_prim} -A ${adapter_3_prim} -G ${adapter_5_prim}" params.trim_quality = "20"
process adaptor_removal_pairedend { params.trimming = "-q ${params.trim_quality},${params.trim_quality}"
container = "${container_url}" params.trimming_out = ""
label "big_mem_mono_cpus" process trimming {
tag "$pair_id"
input:
tuple val(pair_id), path(reads)
output:
tuple val(pair_id), path("*_cut_R{1,2}.fastq.gz"), emit: fastq
path "*_report.txt", emit: report
script:
"""
cutadapt ${params.adaptor_removal_pairedend} \
-o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
params.adaptor_removal_singleend = "-a ${adapter_3_prim} -g ${adapter_5_prim}"
process adaptor_removal_singleend {
container = "${container_url}" container = "${container_url}"
label "big_mem_mono_cpus" label "big_mem_mono_cpus"
tag "$file_id" tag "$file_id"
if (params.trimming_out != "") {
publishDir "results/${params.trimming_out}", mode: 'copy'
}
input: input:
tuple val(file_id), path(reads) tuple val(file_id), path(reads)
output: output:
tuple val(file_id), path("*_cut.fastq.gz"), emit: fastq tuple val(file_id), path("*_trim_R{1,2}.fastq.gz"), emit:fastq
path "*_report.txt", emit: report path "*_report.txt", emit: report
script: script:
""" if (file_id instanceof List){
cutadapt ${params.adaptor_removal_singleend} \ file_prefix = file_id[0]
-o ${file_id}_cut.fastq.gz \ } else {
${reads} > ${file_id}_report.txt file_prefix = file_id
"""
} }
if (reads.size() == 2)
process trimming {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$pair_id"
input:
tuple val(pair_id), path(reads)
output:
tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit:fastq
path "*_report.txt", emit: report
script:
if (reads instanceof List)
""" """
cutadapt -q ${trim_quality},${trim_quality} \ cutadapt ${params.trimming} \
-o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \ -o ${file_id}_trim_R1.fastq.gz -p ${file_id}_trim_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt ${reads[0]} ${reads[1]} > ${file_id}_report.txt
""" """
else else
""" """
cutadapt -q ${trim_quality},${trim_quality} \ cutadapt ${params.trimming} \
-o ${file_id}_trim.fastq.gz \ -o ${file_id}_trim.fastq.gz \
${reads} > ${file_id}_report.txt ${reads} > ${file_id}_report.txt
""" """
} }
process trimming_pairedend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$pair_id"
input:
tuple val(pair_id), path(reads)
output:
tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit:fastq
path "*_report.txt", emit: report
script:
"""
cutadapt -q ${trim_quality},${trim_quality} \
-o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
process trimming_singleend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
input:
tuple val(file_id), path(reads)
output:
tuple val(file_id), path("*_trim.fastq.gz"), emit: fastq
path "*_report.txt", emit: report
script:
"""
cutadapt -q ${trim_quality},${trim_quality} \
-o ${file_id}_trim.fastq.gz \
${reads} > ${file_id}_report.txt
"""
}
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