qbic-pipelines / variantmtb Goto Github PK

Description of feature

since this is not a nf-core pipeline, replace the nfcore logo with the qbic logo.

Issue

• since the template update 2.13.1, the logo is defined in the workflow subworkflos/nf-core/utils_nfcore_pipeline.nf.
• nf-core lint checks integrity of this workflow and fails if changes are made
• other pipelines with custom logos (when it was still defined in lib/nfcoreTemplate.groovy) simply exclude this file from the file_unchanged linting check.
• this is not possible for a (sub)workflow
• no respone on nf-core slack yet

approach

• wait for sarek to perform template update an see how they do it

Please solve the following issues before publishing to master:

• linting
• modules updates
• parameter validation
• make large queries to CGI possible (fail due as a maximum of 2 jobs can run at the same time on the website)

Description of the bug

the github-action test nf-core CI / Run pipeline with test data (21.10.3) fails
the github-action test nf-core CI / Run pipeline with test data passes

mark could replicate the issue on his local machine.
I could not.
I suspect it might be due to querynator depending on packages from conda-forge. I have conda-forge added in my .condarc

Command used and terminal output

Error executing process > 'NFCORE_VARIANTMTB:VARIANTMTB:QUERYNATOR_CIVICAPI (test_sample)'

Caused by:
  Failed to create Conda environment
  command: conda create --mkdir --yes --quiet --prefix /home/runner/work/variantmtb/variantmtb/work/conda/env-8333bfb82ced3d481ee8f58aa4d2aef8 bioconda::querynator=0.4.1
  status : 1
  message:
    PackagesNotFoundError: The following packages are not available from current channels:
    
      - bioconda::querynator==0.4.1
    
    Current channels:
    
      - defaults
      - https://conda.anaconda.org/bioconda

Relevant files

No response

System information

nextflow version 21.10.3

Description of the bug

• fix querynator to handle new cgi wildtype biomarker entry #20
• update conda image
• update querynator modules in variantmtb

Command used and terminal output

No response

Relevant files

No response

System information

No response