feat: Add fasterq-dump module

This commit is contained in:
Thomas A. Christensen II 2023-10-19 11:23:41 -05:00
parent 7e0f64f78b
commit 9f70b504e2
Signed by: millironx
GPG key ID: 09335146883990B9

View file

@ -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"
"""
}