diff --git a/modules/fasterq_dump/main.nf b/modules/fasterq_dump/main.nf new file mode 100644 index 0000000..560d113 --- /dev/null +++ b/modules/fasterq_dump/main.nf @@ -0,0 +1,25 @@ +process FASTERQ_DUMP { + tag "${prefix} (${sra})" + label 'process_single' + + container 'quay.io/biocontainers/sra-tools:3.0.8--h9f5acd7_0' + + input: + tuple val(prefix), val(sra) + + output: + tuple val(prefix), path("*.fastq.gz") + + publishDir "${params.outdir}/${task.process}", mode: 'copy' + + script: + """ + fasterq-dump \\ + --verbose \\ + --concatenate-reads \\ + --stdout \\ + ${sra} \\ + | gzip \\ + > "${prefix}.fastq.gz" + """ +}