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hoelzer-lab / rnaflow

A simple RNA-Seq differential gene expression pipeline using Nextflow
GNU General Public License v3.0
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Error: expression_reference_based:webgestalt (MAQCA_vs_MAQCB) #191

Closed hoelzer closed 2 years ago

hoelzer commented 2 years ago

Hi @fischer-hub !

I'm finally checking and approving the PRs ;)

However, I have in the current master branch now an error running the test command:

nextflow run main.nf -profile local,docker,test -w work -resume

which fails in this step:

[95/f087bc] process > expression_reference_based:webgestalt (MAQCA_vs_MAQCB) [100%] 1 of 1, failed: 1 ✘
Error executing process > 'expression_reference_based:webgestalt (MAQCA_vs_MAQCB)'

Caused by:
  Process `expression_reference_based:webgestalt (MAQCA_vs_MAQCB)` terminated with an error exit status (1)

Command executed:

  R CMD BATCH --no-save --no-restore '--args c(".") c("deseq2_MAQCA_vs_MAQCB_filtered_padj_0.05.csv") c("hsa") c("ensembl_gene_id")' ens_species_mapping.tsv

Command exit status:
  1

I also wonder a bit about the content of the work dir:

ls work/95/f087bcd149215e2b07a698a0cd7993 
deseq2_MAQCA_vs_MAQCB_filtered_padj_0.05.csv  ens_species_mapping.tsv  ens_species_mapping.tsv.Rout

because I would expect also the actual script from the bin/webgestalt.R folder here?

Can you please also give it a try? thx!

fischer-hub commented 2 years ago

Hi @hoelzer, yes I ran into the same issue. Some channel order was wrong resulting in R trying to execute the ens_species_mapping.tsv file. I created a PR with a fix!