mosdepth error on dev branch

[fa2k]

Description of the bug

I'm getting an error from mosdepth in the process NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH on the dev branch.

Command used and terminal output

[fa2k@nepe 0633350f5203e1d7fc8cb896d16d9d]$ cat .command.log 
INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
Usage: mosdepth [options] <prefix> <BAM-or-CRAM>
error parsing arguments


[fa2k@nepe 0633350f5203e1d7fc8cb896d16d9d]$ cat .command.sh
#!/bin/bash -euo pipefail
mosdepth \
    --threads 6 \
     \
    --fasta genome.fa \
    --d4 \
    NA12878_mosdepth \
    NA12878_sorted_md.bam

cat <<-END_VERSIONS > versions.yml
"NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH":
    mosdepth: $(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*$//')
END_VERSIONS

Relevant files

No response

System information

No response

[fa2k]

Seems like mosdepth v0.3.8 in the docker and apptainer containers doesn't support the --d4 option. I don't see anything in mosdepth's repo indicating that they dropped support for this. It works in the v0.3.6 container. I'm not even able to install the conda versions.

[jemten]

Yeah, We've had to add this to our in-house config

    withName: '.*QC_BAM:MOSDEPTH' {
        container = 'https://depot.galaxyproject.org/singularity/mosdepth%3A0.3.3--hd299d5a_3'
    }

You can do the same with 0.3.6

There is an 0.3.9 version of mosdepth which looks like it includes som fixes for d4, https://github.com/brentp/mosdepth/releases/tag/v0.3.9. But that version isn't on conda.

[fa2k]

Yes, overriding the mosdepth images works well, thanks for the tip :) don't know if this is a bug in the mosdepth image. We can surely test the new version when it comes to conda and biocontainers.