nf-core modules update --all

[maxulysse]

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 - add to the software_versions process and a regex to scrape_software_versions.py
  • 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/sarek 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).
• 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).

[FriederikeHanssen]

Hm, prematurely approved 😆 somethiing off with the target bed:

=================================== FAILURES ===================================
_________________________________ test session _________________________________
'Run default pipeline with target bed' exited with exit code '1' instead of '0'.
=========================== short test summary info ============================
FAILED tests/test_targeted.yml::Run default pipeline with target bed::exit code should be 0
=================== 1 failed, 21 passed in 292.13s (0:04:52) ===================
Error: Process completed with exit code 1.

[FriederikeHanssen]

Maybe the tabix module?

[maxulysse]

Maybe the tabix module?

I'll investigate

[FriederikeHanssen]

The last test fails tests/test_targeted.yml .....................F are they checked by order in the yaml? Then it should be the - path: results/reports/samtools_stats/1234N/1234N.recal.cram.stats file 🤔 . But that module is not updated 😕

[maxulysse]

I reverted the tabix modules update, and it works.
I'm assuming there's some changes there that impact the rest of the downstream analysis.

[maxulysse]

I fixed some issues with the names of the files for the tabix modules.
I'll figure the tabix modules update in a separate PR.