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DSL2: add reference masking for PMDtools #1030

Merged
merged 8 commits into from
Dec 8, 2023
Merged

DSL2: add reference masking for PMDtools #1030

merged 8 commits into from
Dec 8, 2023

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scarlhoff
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@scarlhoff scarlhoff commented Oct 27, 2023 •
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This adds the options to run PMDtools only on a specific part of the genome within the damage manipulation subworkflow. Input options are the mapping reference, an already masked fasta file and a bed file for masking of the mapping reference.
This closes #1029.

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/eager 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 Nov 10, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a62d332

+| ✅ 159 tests passed       |+
!| ❗  20 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • 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 nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • 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 test_humanbam.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_humanbam.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowEager.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • schema_description - No description provided in schema for parameter: skip_qualimap
  • schema_description - No description provided in schema for parameter: skip_damage_calculation

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-07 09:05:59

@scarlhoff scarlhoff marked this pull request as ready for review November 10, 2023 13:48
@scarlhoff scarlhoff requested a review from a team November 10, 2023 13:48
@scarlhoff scarlhoff linked an issue Nov 10, 2023 that may be closed by this pull request
DSL2: add reference masking for PMDtools #1029
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jfy133
jfy133 approved these changes Nov 10, 2023
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From my phone so not tested, but theoretically looks good :)

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TCLamnidis
TCLamnidis requested changes Nov 16, 2023
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@scarlhoff scarlhoff requested a review from TCLamnidis November 24, 2023 09:02
TCLamnidis
TCLamnidis approved these changes Dec 5, 2023
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One minor helptext suggestion, but otherwise LGTM!

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@TCLamnidis TCLamnidis closed this Dec 6, 2023
@TCLamnidis TCLamnidis reopened this Dec 6, 2023
@scarlhoff scarlhoff merged commit 7ac6cb0 into nf-core:dev Dec 8, 2023
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@scarlhoff scarlhoff deleted the dsl2_pmd_maskedfasta branch August 9, 2024 09:27
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@TCLamnidis TCLamnidis TCLamnidis approved these changes

@jfy133 jfy133 jfy133 approved these changes

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DSL2: add reference masking for PMDtools
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@scarlhoff @jfy133 @TCLamnidis