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/*
* cutadapt :
* Imputs : fastq files
*/
/*
* for paired-end data
*/
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
log.info "fastq files : ${params.fastq}"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process adaptor_removal {
tag "$pair_id"
input:
set pair_id, file(reads) from fastq_files
output:
file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
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script:
"""
cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
-o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
/*
* for single-end data
*/
params.fastq = "$baseDir/data/fastq/*.fastq"
log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process adaptor_removal {
tag "$reads.baseName"
input:
file reads from fastq_files
output:
file "*_cut.fastq.gz" into fastq_files_cut
script:
"""
cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
-o ${reads.baseName}_cut.fastq.gz \
${reads} > ${reads.baseName}_report.txt
"""
}
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/* quality trimming */
/*
* for paired-end data
*/
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
log.info "fastq files : ${params.fastq}"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process trimming {
tag "$pair_id"
input:
set pair_id, file(reads) from fastq_files
output:
file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
script:
"""
cutadapt -q 20,20 \
-o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
/*
* for single-end data
*/
params.fastq = "$baseDir/data/fastq/*.fastq"
log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process trimming {
tag "$reads.baseName"
input:
file reads from fastq_files
output:
file "*_trim.fastq.gz" into fastq_files_cut
script:
"""
cutadapt -q 20,20 \
-o ${reads.baseName}_trim.fastq.gz \
${reads} > ${reads.baseName}_report.txt
"""
}