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Fix null value for joint calling with Mutect2 #1277

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merged 5 commits into from
Oct 11, 2023
Merged

Fix null value for joint calling with Mutect2 #1277

merged 5 commits into from
Oct 11, 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 Oct 10, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2db3cbd

+| ✅ 147 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-11 08:14:22

maxulysse
maxulysse approved these changes Oct 11, 2023
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LGTM

@FriederikeHanssen
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Manual tests passed:


(nf-core) [iizha01@rddsws sarek]$ TEST_DATA_BASE=mutect2_manual TMPDIR=~ PROFILE=docker pytest --tag mutect2_manual --symlink --keep-workflow-wd --git-aware
========================================================================================== test session starts ===========================================================================================
platform linux -- Python 3.6.13, pytest-6.2.3, py-1.11.0, pluggy-0.13.1
rootdir: /home/iizha01/sarek
plugins: workflow-1.6.0
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: /home-link/iizha01/pytest_workflow_64xtezmn/Run_variant_calling_on_somatic_sample_with_mutect2_without_intervals
        stdout:    /home-link/iizha01/pytest_workflow_64xtezmn/Run_variant_calling_on_somatic_sample_with_mutect2_without_intervals/log.out
        stderr:    /home-link/iizha01/pytest_workflow_64xtezmn/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: /home-link/iizha01/pytest_workflow_64xtezmn/Run_variant_calling_on_somatic_sample_with_mutect2
        stdout:    /home-link/iizha01/pytest_workflow_64xtezmn/Run_variant_calling_on_somatic_sample_with_mutect2/log.out
        stderr:    /home-link/iizha01/pytest_workflow_64xtezmn/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: /home-link/iizha01/pytest_workflow_64xtezmn/Run_joint_calling_on_tumor_only_samples_with_mutect2
        stdout:    /home-link/iizha01/pytest_workflow_64xtezmn/Run_joint_calling_on_tumor_only_samples_with_mutect2/log.out
        stderr:    /home-link/iizha01/pytest_workflow_64xtezmn/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: /home-link/iizha01/pytest_workflow_64xtezmn/Run_joint_calling_on_somatic_samples_with_mutect2
        stdout:    /home-link/iizha01/pytest_workflow_64xtezmn/Run_joint_calling_on_somatic_samples_with_mutect2/log.out
        stderr:    /home-link/iizha01/pytest_workflow_64xtezmn/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.


==================================================================================== 132 passed in 3544.50s (0:59:04) ====================================================================================

Just waiting for confirmation from @berguner

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My tests using in-house data also worked. Thanks for the quick fix @FriederikeHanssen ! 👍

@FriederikeHanssen
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FriederikeHanssen commented Oct 11, 2023 •
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yay 🥳 ok merging then. And thanks for investigating where the issue is in the first place 🙏

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review October 11, 2023 10:09
@FriederikeHanssen FriederikeHanssen merged commit 31aefde into nf-core:dev Oct 11, 2023
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@FriederikeHanssen FriederikeHanssen mentioned this pull request Oct 11, 2023
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@FriederikeHanssen @berguner @maxulysse