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DSL2: Add rg info to BWA_MEM #1046

Merged
merged 1 commit into from
Feb 8, 2024
Merged

DSL2: Add rg info to BWA_MEM #1046

merged 1 commit into from
Feb 8, 2024

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TCLamnidis
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@TCLamnidis TCLamnidis commented Feb 7, 2024 •
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The modules.config for this one was lacking any RG tag info.

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).

@TCLamnidis TCLamnidis changed the base branch from master to dev February 7, 2024 15:49
@nf-core nf-core deleted a comment from github-actions bot Feb 7, 2024
@TCLamnidis TCLamnidis closed this Feb 7, 2024
@TCLamnidis TCLamnidis reopened this Feb 7, 2024
@TCLamnidis TCLamnidis requested review from jfy133 and a team February 7, 2024 15:51
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github-actions bot commented Feb 7, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b6cf17e

+| ✅ 233 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  20 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • 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 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.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 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 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 WorkflowEager.groovy: Optionally add in-text citation tools to this list.
  • 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
  • schema_description - No description provided in schema for parameter: skip_qualimap
  • schema_description - No description provided in schema for parameter: skip_damage_calculation

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.contamination_estimation_angsd_hapmap

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-07 15:53:16

@TCLamnidis TCLamnidis mentioned this pull request Feb 7, 2024
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@nf-core nf-core deleted a comment from github-actions bot Feb 8, 2024
scarlhoff
scarlhoff reviewed Feb 8, 2024
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The code to include looks fine to me, but is hardcoded for Illumina sequencing. As specified in #970, we want to provide the option to specify the sequencing platform in 3.0. Might be easier to change all mappers at once though.

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TCLamnidis commented Feb 8, 2024 •
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I would leave that for when that option gets implemented, indeed.

PR checs are failing cause of branch protection, which I have fixed but have no further commits, so will go ahead and merge.

@TCLamnidis TCLamnidis merged commit 2a10626 into dev Feb 8, 2024
16 of 17 checks passed
@TCLamnidis TCLamnidis deleted the add_bwamem_rg branch February 8, 2024 14:06
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@jfy133 jfy133 Awaiting requested review from jfy133

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