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

[eduard-watchmaker]

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

Removed and added to specific subworkflow tests directives!

[eduard-watchmaker]

The Channel.empty() works with my tests, the mentioned [[:], [] ] did not, so I kept as it.

Thanks again for your time and review.

[eduard-watchmaker]

@Joon-Klaps any thoughts on the state of the branch?

[Joon-Klaps]

@nf-core-bot update gpu snapshot path: subworkflows/nf-core/fastq_align_dedup_bwamem

[Joon-Klaps]

@eduard-watchmaker, seems like the gpu snapshot files are still empty. This is likely becuase you've provided Channel.empty() as an input. Whenever a nextflow process recevies an Channel.empty(), it doesn't get executed. There is a difference between Channel.of([[:], []]) and Channel.empty().

I'm suprised to hear that [[:], []] didn't work, as it's the default way of providing empty inputs. Why didn't it work?

Also you didn't adress this https://github.com/nf-core/modules/pull/9309/files#r2485746222.

[eduard-watchmaker]

@eduard-watchmaker, seems like the gpu snapshot files are still empty. This is likely becuase you've provided Channel.empty() as an input. Whenever a nextflow process recevies an Channel.empty(), it doesn't get executed. There is a difference between Channel.of([[:], []]) and Channel.empty().

I'm suprised to hear that [[:], []] didn't work, as it's the default way of providing empty inputs. Why didn't it work?

Also you didn't adress this https://github.com/nf-core/modules/pull/9309/files#r2485746222.

I keep getting the: Caused by: Path value cannot be null

but that may actually not be the reason of it, although I can't find the culprit at all.

[famosab]

Ah yes the bwa/index issue I suspect. See github.com/nf-core/modules/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[bot]]

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