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nf-core / viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples
https://nf-co.re/viralrecon
MIT License
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`MOSDEPTH_AMPLICON` doesn't run in `dev` branch #419

Closed tavareshugo closed 7 months ago

tavareshugo commented 9 months ago

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 commented 7 months ago

Good spot! Thanks a lot @tavareshugo for this! It seems to be fixed in this PR https://github.com/nf-core/viralrecon/pull/401