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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
#==============================================
code documentation
#==============================================
*/
/*
#==============================================
params
#==============================================
*/
params.saveMode = 'copy'
params.filePattern = "./*_{R1,R2}.fastq.gz"
params.resultsDir = 'results/trimmomatic'
Channel.fromFilePairs(params.filePattern)
.into { ch_in_trimmomatic }
/*
#==============================================
trimmomatic
#==============================================
*/
process trimmomatic {
publishDir params.resultsDir, mode: params.saveMode
container 'quay.io/biocontainers/trimmomatic:0.35--6'
input:
tuple genomeName, file(genomeReads) from ch_in_trimmomatic
output:
tuple path(fq_1_paired), path(fq_2_paired) into ch_out_trimmomatic
script:
fq_1_paired = genomeName + '_R1.p.fastq'
fq_1_unpaired = genomeName + '_R1.s.fastq'
fq_2_paired = genomeName + '_R2.p.fastq'
fq_2_unpaired = genomeName + '_R2.s.fastq'
"""
trimmomatic \
PE -phred33 \
${genomeReads[0]} \
${genomeReads[1]} \
$fq_1_paired \
$fq_1_unpaired \
$fq_2_paired \
$fq_2_unpaired \
LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36
"""
}
/*
#==============================================
# extra
#==============================================
*/