/* * urqt : * Imputs : fastq files * Output : fastq files */ /* 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" cpus 4 publishDir "results/fastq/trimming/", mode: 'copy' input: set pair_id, file(reads) from fastq_files output: file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut script: """ UrQt --t 20 --m ${task.cpus} --gz \ --in ${reads[0]} --inpair ${reads[1]} \ --out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \ > ${pair_id}_trimming_report.txt """ } /* * for single-end data */ params.fastq = "$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" cpus 4 publishDir "results/fastq/trimming/", mode: 'copy' input: file reads from fastq_files output: file "*_trim.fastq.gz" into fastq_files_trim script: """ UrQt --t 20 --m ${task.cpus} --gz \ --in ${reads} \ --out ${reads.baseName}_trim.fastq.gz \ > ${reads.baseName}_trimming_report.txt """ }