MOSDEPTH_AMPLICON doesn't run in dev branch

[tavareshugo]

Description of the bug

In the current dev branch the modules MOSDEPTH_AMPLICON and PLOT_MOSDEPTH_REGIONS_AMPLICON seem to be always skipped.

This may be related to these changes.
I'm sorry, I'm not familiar with the syntax, but maybe @svarona can spot what might be the issue?

The commands I used to test:

# current version
nextflow run viralrecon -r 2.6.0 -profile test,singularity --outdir results/v2.6 --skip_assembly --skip_asciigenome --skip_consensus

# development version
nextflow run viralrecon -r dev -profile test,singularity --outdir results/dev --skip_assembly --skip_asciigenome --skip_consensus --skip_freyja

(I've skipped several steps to save time for testing)

Both run successfully (i.e. there is no error), but the second one does not run the MOSDEPTH_AMPLICON processes.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[svarona]

Good spot! Thanks a lot @tavareshugo for this! It seems to be fixed in this PR #401