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Dummy PR : testing docker container options in GATK Spark modules #1430

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2 commits merged into from Mar 8, 2024
Merged

Dummy PR : testing docker container options in GATK Spark modules #1430

2 commits merged into from Mar 8, 2024

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@asp8200 asp8200 commented Mar 4, 2024 •
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Testing docker container options in GATK Spark modules. - Just a dummy PR for discussion and triggering CI-tests.

In this PR, I made changes to the modules (like Jonas did). However, I would prefer a solution where we don't change the modules but just alter the containerOptions in the corresponding config.

If we're to update the modules, then I guess they should first be updated in the modules-repo? (Or are we perhaps going to make a "local" patch of the Spark modules?)

Note that the following (silly) test of joint-germline with profile use_gatk_spark also work on this PR:

NXF_VER=24.01.0-edge PROFILE=docker nextflow run main.nf -profile test_cache,targeted,use_gatk_spark --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --known_snps_vqsr false --known_indels_vqsr false

(The test is "silly" because it doesn't actually call any Spark modules.)

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github-actions bot commented Mar 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ea92fd7

+| ✅ 181 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-04 22:11:22

@asp8200 asp8200 mentioned this pull request Mar 7, 2024
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@asp8200 asp8200 closed this pull request by merging all changes into nf-core:dev in 2e06e65 Mar 8, 2024
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asp8200 commented Mar 21, 2024

@maxulysse : This solution also works with awsbatch and Spark.

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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen will be requested when the pull request is marked ready for review FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse will be requested when the pull request is marked ready for review maxulysse is a code owner

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