When running the pipeline with --skip_clipping and --keep_phix: ERROR ~ No such variable: ch_phix_db_file

[amizeranschi]

Hello,

When running the pipeline as such:

nextflow run nf-core/mag -r 3.3.0 \
-profile docker,test \
--skip_clipping \
--keep_phix \
--skip_spades \
--skip_prodigal \
--skip_prokka \
--skip_metaeuk \
--skip_binning \
--skip_gtdbtk \
--outdir test-mag-3.3.0

I'm getting the following error:

ERROR ~ No such variable: ch_phix_db_file

 -- Check script '/home/amizeranschi/.nextflow/assets/nf-core/mag/./workflows/mag.nf' at line: 161 or see '.nextflow.log' file for more details

The log file is attached.

.nextflow.log

[jfy133]

Thanks for the report @amizeranschi ! I'm back from holiday now so will investigate ASAP.

I think this is likely an edge case not come up during the testing of the recent refactoring of the module code into subworkflows by @muabnezor

[muabnezor]

Yes, you're right @jfy133 . Fix to bug in PR #718