Bump Samtools to v1.24

[matthdsm]

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.
• Broadcast software version numbers to topic: versions - See version_topics
• 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

[mashehu]

too fast! there is a PR to make your life easier in the pipeline nf-core/tools#4374

[matthdsm]

Samtools waits for no man!
Also, this release features my first contribution to samtools, which I've kind of wanted for a while 😄

[mashehu]

Congrats! (now you can time then even better with hackathons 😉)

[matthdsm]

Sadly I have no control over release timings 😅 Otherwise I'd release ALL the tools during the hackathon. Give people smth to do

[matthdsm]

SOOOOOO many broken tests 😲

[matthdsm]

@nf-core-bot update gpu snapshot path: subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test

[matthdsm]

Some failures remain:

• singularity containers have no gzip for some reason 🤔
• subwf using bwa_align keep failing, even though the tests pass locally

[maxulysse]

Still a linting issue for samtools/bam2fq

[maxulysse]

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