Help running in offline cluster

[telatin]

I need to run mag in offline mode and I tried with:

nextflow run $NF/nextflow/nf-core-mag-1.0.0/workflow/main.nf \
  --reads '$INPUT/reads/*_R{1,2}.fq.gz' \
  --busco_reference $DB/bacteria_odb9.tar.gz \
  --outdir out \
  --cat_db $DB/CAT_prepare_20190108.tar.gz \
  --kraken2_db $DB/minikraken2_v2_8GB_201904_UPDATE.tgz \
  --centrifuge_db $DB/p_compressed+h+v.tar.gz \
  -profile singularity

But I got an error from the KronaDB updater:

Caused by:
  Process `krona_db` terminated with an error exit status (1)

Command executed:
  ktUpdateTaxonomy.sh taxonomy

Command exit status:
  1

Command output:
  Creating taxonomy...
  
  Fetching taxdump.tar.gz...
  
  Update failed.
     Is your internet connection okay?

Command error:
  /opt/conda/envs/nf-core-mag-1.0.0/bin/ktUpdateTaxonomy.sh: line 163: [: ==: unary operator expected

Work dir:
  /qib/platforms/Informatics/GMH/nextflow/work/86/ca13b3e7b7dcc86ba54cb03e2f0d1b

I'd like to skip the ktUpdateTaxonomy.sh without skipping Krona plots, how can I do the step in advance (if required) and then run the workflow from the cluster? Thanks

[HadrienG]

At the moment you can't run krona in offline mode, that's an oversight on our part. I'll put this on the 1.1.0 release that should be out soon.

Thanks for bringing this up!

[telatin]

Ok thanks! I made a small change in the code to provide a taxonomy file in the meanwhile.

[d4straub]

@HadrienG any progress here?