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Version bumped bwa/index and bwa/aln #5613

Merged
merged 2 commits into from
May 20, 2024
Merged

Version bumped bwa/index and bwa/aln #5613

merged 2 commits into from
May 20, 2024

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GallVp
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@GallVp GallVp commented May 16, 2024

PR checklist

Closes #XXX

  • Version bumped bwa/index and bwa/aln
  • 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

@GallVp
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GallVp commented May 16, 2024

The reason for the PR is this issue with the older version biocontainer:

Unable to find image 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7' locally
0.7.17--hed695b0_7: Pulling from biocontainers/bwa
docker: [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/biocontainers/bwa:0.7.17--hed695b0_7 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/.
See 'docker run --help'.

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@jfy133 jfy133 left a comment

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LGTM

@GallVp GallVp enabled auto-merge May 16, 2024 08:36
@SPPearce
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Conda has different md5sums on the bam files as usual, so need to check existence for those rather than contents

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LGTM with the tests passing 👍

@SPPearce SPPearce added this pull request to the merge queue May 20, 2024
Merged via the queue into nf-core:master with commit 086fa66 May 20, 2024
41 checks passed
tstoeriko pushed a commit to tstoeriko/nf-core-modules that referenced this pull request May 22, 2024
* Version bumped bwa/index and bwa/aln

* Removed bam md5sum from snapshot
@GallVp GallVp deleted the bwa branch May 28, 2024 23:55
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4 participants