/* * sra-tools : */ /* fastq-dump * Imputs : srr list * Outputs : fastq files */ params.list_srr = "$baseDir/data/SRR/*.txt" log.info "downloading list srr : ${params.list_srr}" Channel .fromPath( params.list_srr ) .ifEmpty { error "Cannot find any bam files matching: ${params.list_srr}" } .splitCsv(header: true) .set { SRR } //run is the column name containing SRR ids process fastq-dump { tag {"${x.run}"} publishDir "results/download/fastq/${x.run}/", mode: 'copy' input: val x from SRR output: file("*") into fastq script: """ fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" ${x.run} if [ -f ${x.run}_1.fastq ] then true else touch ${x.run}.fastq fi """ }