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fix getpileupsummary should not run if no germline resource is provided #1171

Merged
merged 11 commits into from
Aug 17, 2023
Merged

fix getpileupsummary should not run if no germline resource is provided #1171

merged 11 commits into from
Aug 17, 2023

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FriederikeHanssen
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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/sarek 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>).
  • 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).

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github-actions bot commented Aug 4, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aaa1f63

+| ✅ 151 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-16 08:48:25

@FriederikeHanssen
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Don't merge yet, running manual test!

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FriederikeHanssen commented Aug 5, 2023 •
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Results from manual run:

gitpod /workspace/sarek (germline_resource) $ PROFILE=docker pytest --tag mutect2_manual --symlink --keep-workflow-wd
================================================================================================================================ test session starts =================================================================================================================================
platform linux -- Python 3.10.12, pytest-7.4.0, pluggy-1.2.0
rootdir: /workspace/sarek
plugins: workflow-2.0.1
collecting ... 
collected 132 items                                                                                                                                                                                                                                                                  

Run variant calling on somatic sample with mutect2 without intervals:
        command:   nextflow run main.nf -profile test_cache,tools_somatic --tools mutect2 --no_intervals --outdir results
        directory: /tmp/pytest_workflow_ltedllvb/Run_variant_calling_on_somatic_sample_with_mutect2_without_intervals
        stdout:    /tmp/pytest_workflow_ltedllvb/Run_variant_calling_on_somatic_sample_with_mutect2_without_intervals/log.out
        stderr:    /tmp/pytest_workflow_ltedllvb/Run_variant_calling_on_somatic_sample_with_mutect2_without_intervals/log.err
'Run variant calling on somatic sample with mutect2 without intervals' done.

Run variant calling on somatic sample with mutect2:
        command:   nextflow run main.nf -profile test_cache,tools_somatic --tools mutect2 --outdir results
        directory: /tmp/pytest_workflow_ltedllvb/Run_variant_calling_on_somatic_sample_with_mutect2
        stdout:    /tmp/pytest_workflow_ltedllvb/Run_variant_calling_on_somatic_sample_with_mutect2/log.out
        stderr:    /tmp/pytest_workflow_ltedllvb/Run_variant_calling_on_somatic_sample_with_mutect2/log.err
'Run variant calling on somatic sample with mutect2' done.

Run joint calling on tumor only samples with mutect2:
        command:   nextflow run main.nf -profile test_cache,tools_tumoronly --input tests/csv/3.0/recalibrated_tumoronly_joint.csv --tools mutect2 --joint_mutect2 --outdir results
        directory: /tmp/pytest_workflow_ltedllvb/Run_joint_calling_on_tumor_only_samples_with_mutect2
        stdout:    /tmp/pytest_workflow_ltedllvb/Run_joint_calling_on_tumor_only_samples_with_mutect2/log.out
        stderr:    /tmp/pytest_workflow_ltedllvb/Run_joint_calling_on_tumor_only_samples_with_mutect2/log.err
'Run joint calling on tumor only samples with mutect2' done.

Run joint calling on somatic samples with mutect2:
        command:   nextflow run main.nf -profile test_cache,tools_somatic --input tests/csv/3.0/recalibrated_somatic_joint.csv --tools mutect2 --joint_mutect2 --outdir results
        directory: /tmp/pytest_workflow_ltedllvb/Run_joint_calling_on_somatic_samples_with_mutect2
        stdout:    /tmp/pytest_workflow_ltedllvb/Run_joint_calling_on_somatic_samples_with_mutect2/log.out
        stderr:    /tmp/pytest_workflow_ltedllvb/Run_joint_calling_on_somatic_samples_with_mutect2/log.err
'Run joint calling on somatic samples with mutect2' done.

tests/test_tools_manually.yml ....................................................................................................................................                                                                                                             [100%] Keeping temporary directories and logs. Use '--kwd' or '--keep-workflow-wd' to disable this behaviour.


================================================================================================================================== warnings summary ==================================================================================================================================
../../opt/conda/lib/python3.10/site-packages/pytest_workflow/plugin.py:397
  /opt/conda/lib/python3.10/site-packages/pytest_workflow/plugin.py:397: UserWarning: .git dir detected: /workspace/sarek/.git. pytest-workflow will copy the entire .git directory and all files ignored by git. It is recommended to use the --git-aware option.
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
==================================================================================================================== 132 passed, 1 warning in 5738.45s (1:35:38) =====================================================================================================================

maxulysse
maxulysse reviewed Aug 15, 2023
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@FriederikeHanssen
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Still waiting for an answer from Thomas. All my tests on real data with his parameters work as intended though

FriederikeHanssen and others added 2 commits August 16, 2023 10:39
@FriederikeHanssen @maxulysse
Update workflows/sarek.nf
1f5e174 
Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>
@FriederikeHanssen
Merge branch 'dev' into germline_resource
aaa1f63
@FriederikeHanssen FriederikeHanssen merged commit 66af584 into nf-core:dev Aug 17, 2023
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@FriederikeHanssen @maxulysse @asp8200