Qualimap protocol parameter not passed

[ameynert]

Running with --reverseStranded, the Qualimap .command.sh looks like this:

#!/bin/bash -euo pipefail
unset DISPLAY
qualimap --java-mem-size=8G rnaseq strand-specific-reverse -pe -s -bam sample.sortedByCoord.out.bam -gtf Homo_sapiens.GRCh38.99.gtf -outdir sample.sortedByCoord.out

It's missing the '-p' in front of strand-specific-reverse.

Output:

    bam file = sample.sortedByCoord.out.bam
    gff file = Homo_sapiens.GRCh38.99.gtf
    counting algorithm = uniquely-mapped-reads
    protocol = non-strand-specific

Should be protocol = strand-specific-reverse

[RoganGrant]

I noticed the same issue with reverse stranding, single-end data

[apeltzer]

Double checked and the current dev branch doesn't show this anymore 👍 So closing this :-)

[apeltzer]

Proof: https://github.com/nf-core/rnaseq/blob/dev/main.nf#L1489