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Update last/* modules to version 1611 from version 1608. #7762

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merged 2 commits into from
Mar 11, 2025

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@charles-plessy charles-plessy commented Mar 10, 2025

For last/mafconvert, this is an important update that fixes a bug where long hard-clipping lengths in CIGAR lines would go over the maximal limit of 268435455 for BAM and CRAM files.

Other modules are also updated for the sake of consistency but there should be no difference other than MD5 sums changing in files that contain the version number.

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

For `last/mafconvert`, this is an important update that fixes a bug
where long hard-clipping lengths in CIGAR lines would go over the
maximal limit of 268435455 for BAM and CRAM files.

Other modules are also updated for the sake of consistency but there
should be no difference other than MD5 sums changing in files that
contain the version number.
@charles-plessy charles-plessy force-pushed the last_update_to_1611 branch 6 times, most recently from adc0cd6 to 1b2ff26 Compare March 10, 2025 05:10
@SPPearce SPPearce added this pull request to the merge queue Mar 11, 2025
Merged via the queue into master with commit 0723b03 Mar 11, 2025
98 checks passed
@SPPearce SPPearce deleted the last_update_to_1611 branch March 11, 2025 09:10
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