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Use jq sequera containers #28

Merged
merged 3 commits into from
Dec 18, 2024
Merged

Use jq sequera containers #28

merged 3 commits into from
Dec 18, 2024

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charles-plessy
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@charles-plessy charles-plessy commented Dec 18, 2024 •
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Current CI on master fails because jq 1.6 is not available in bioconda.

Switching to sequera containers solves that problem.

PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/pairgenomealign branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

charles-plessy and others added 2 commits December 18, 2024 10:57
@charles-plessy
Downgrade jq to version 1.5.
c8dc0f3 
Only this version is simultaneously available for Conda, Docker and
Singularity.

The local module only uses `jq -r` which is a simple command with
same output in 1.5 and 1.6.
@sateeshperi
use seqera container for jq local module
20e5e0d
@charles-plessy charles-plessy changed the title Downgrade jq to version 1.5. Use jq sequera containers Dec 18, 2024
@sateeshperi sateeshperi merged commit 75ea4d4 into dev Dec 18, 2024
6 checks passed
@sateeshperi sateeshperi deleted the fix_conda_env_for_local_module branch December 18, 2024 07:02
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@sateeshperi sateeshperi sateeshperi approved these changes

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@charles-plessy @sateeshperi