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Feature/manta #69

Merged
merged 14 commits into from
Dec 21, 2021
Merged

Feature/manta #69

merged 14 commits into from
Dec 21, 2021

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ramprasadn
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@ramprasadn ramprasadn commented Dec 16, 2021 •
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adds manta sv caller subworkflow

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/raredisease 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).
  • 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 Dec 16, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1acf717

+| ✅ 137 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  16 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Update the example "typical command" below used to run the pipeline
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2021-12-21 15:13:26

@ramprasadn ramprasadn linked an issue Dec 16, 2021 that may be closed by this pull request
add manta to SV caller subworkflow #59
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@ramprasadn ramprasadn marked this pull request as ready for review December 20, 2021 10:39
jemten
jemten approved these changes Dec 21, 2021
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Looks good to me. Any comments from @projectoriented

workflows/raredisease.nf Show resolved Hide resolved
subworkflows/local/call_sv_manta.nf
Comment on lines +29 to +31
} else {
ch_target_bed = ch_bed.ifEmpty([[],[],[]])
MANTA ( manta_input_bams, bai_file_list, fasta, fai, ch_target_bed )
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Just a comment that we can adress in a later PR. As the model is written if WES has been set and no target bed file has been given, manta will be executed in WGS mode. There should be check to see that a target file has been given if wes mode is active. However that check shouldn't be here.

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Good point! I'll do that in a different PR.

@ramprasadn ramprasadn merged commit 2c4bc1f into nf-core:dev Dec 21, 2021
@ramprasadn ramprasadn deleted the feature/manta branch December 21, 2021 15:48
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@jemten jemten jemten approved these changes

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add manta to SV caller subworkflow
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@ramprasadn @jemten @projectoriented