moved CGI credentials to nf secrets

[HomoPolyethylen]

CGI credentials used to be pipeline param, moved to nextflow secrets, so that credentials are not open readable.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/variantmtb branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[HomoPolyethylen]

nf-core CI / Run pipeline with test data (21.10.3) fails:

Error mesage

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

had this issue before, if I remember correctly, adding conda-forge resolved it

[mapo9]

very nice!
Famke should have a look as well I think

[famosab]

👍

[famosab]

Looks good to me.

We just need to fix the CI stuff. Do we know why Python 3.6 is used?

[mapo9]

thanks Famke.
Niclas, maybe you can add the problems that occured to the issue that already exists with the ToDos
LGTM then 🚀

[mapo9]

nice fix!
LGTM
let's merge