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Fix datapath in nftests #1426

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merged 22 commits into from
Mar 1, 2024
Merged

Fix datapath in nftests #1426

merged 22 commits into from
Mar 1, 2024

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asp8200
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@asp8200 asp8200 commented Feb 27, 2024 •
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#1425 (Implicitly #1406)

Also fixing docker.runOptions in test-configs and profile config for GATK Spark, since it doesn't have support for docker.userEmulation. See #1405 (comment).

All tests pass with docker.runOptions = { params.use_gatk_spark ? '' : '-u $(id -u):$(id -g)' }.call(). However, the following command, which is the joint-germline test-cmd plus GATK-spark, fails :

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

Now there is not much point in specifying the profile use_gatk_spark for a command like that, since it doesn't use GATK-spark modules. However, the same cmd but with NXF_VER=23.04.0 works on the master branch.

The pytests and the above test-cmd all work if I do

docker.runOptions = { params.use_gatk_spark ? '-u $(id -u):$(id -g) -v /etc/passwd:/etc/passwd:ro ' : '-u $(id -u):$(id -g)' }.call()

TO-DO: Remove temporary tag foo.

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github-actions bot commented Feb 27, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ece0430

+| ✅ 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 2024-03-01 13:14:50

@asp8200 asp8200 mentioned this pull request Feb 27, 2024
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@asp8200 asp8200 marked this pull request as ready for review February 27, 2024 17:25
@asp8200 asp8200 requested review from FriederikeHanssen and matthdsm and removed request for FriederikeHanssen February 27, 2024 17:25
maxulysse
maxulysse reviewed Feb 28, 2024
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asp8200
asp8200 commented Feb 28, 2024
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asp8200
asp8200 commented Feb 28, 2024
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asp8200
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pontus
pontus previously approved these changes Feb 28, 2024
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maxulysse
maxulysse reviewed Mar 1, 2024
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@maxulysse maxulysse merged commit 355c354 into nf-core:dev Mar 1, 2024
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@maxulysse maxulysse maxulysse approved these changes

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@matthdsm matthdsm Awaiting requested review from matthdsm

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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