bump samtools

[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.
• 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

[SPPearce]

You'll need to update every single test because they have the md5sum of the versions 😞

[matthdsm]

I know...
Nothing a little for-loop can't handle!

[matthdsm]

conda!! 😠

[famosab]

It is only the pytest ones that are failing, right? Maybe just move the tests to nf-test. (samtools/markdup, samtools/reheader)
Edit: and the one for bam_stats_samtools (subworkflow)

[SPPearce]

It is only the pytest ones that are failing, right? Maybe just move the tests to nf-test. (samtools/markdup, samtools/reheader) Edit: and the one for bam_stats_samtools (subworkflow)

They both look pretty simple to swap to nf-test, I'll try and fit it in later if nobody has done before then. Although I don't know why markdup is currently using samtools collate first, that seems unnecessary.