Add fq2bam fq align dd bwamem

[eduard-watchmaker]

PR checklist

Closes #XXX

• 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 module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[Joon-Klaps]

The changes in nf-test.config is something that needs to be double checked.

[eduard-watchmaker]

The changes in nf-test.config is something that needs to be double checked.

Removed and added to specific subworkflow tests directives!

[Joon-Klaps]

Sorry, quite a few things I should have spotted in the first round.

[famosab]

Ah yes the bwa/index issue I suspect. See github.com//issues/9230 for the ongoing discussion.

[eduard-watchmaker]

Ah yes the bwa/index issue I suspect. See github.com//issues/9230 for the ongoing discussion.

I assume these tests were running on the original version of fq2bam? Unsure why they are not working now with the samew bwa mem issue.

[eduard-watchmaker]

Very unsure about what is going on with the singularity / apptainer profile here, any thoughts @famosab @Joon-Klaps ?

[eduard-watchmaker]

@nf-core-bot update gpu snaphost path: subworkflows/nf-core/fastq_align_dedup_bwamem/tests/gpu.nf.test

[eduard-watchmaker]

@nf-core-bot fix linting

[eduard-watchmaker]

@nf-core-bot fix linting

[eduard-watchmaker]

@nf-core-bot fix linting

[github-actions]

Nothing for me to do here! 🤷
This is probably because the linting errors come from nf-core lint and have to be fixed manually (or with nf-core lint --fix).