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renamed bwa_index to bwa in subworkflow #27

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@daisymut daisymut commented Feb 2, 2024

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/sammyseq 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 Feb 2, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 97e074a

+| ✅ 165 tests passed       |+
!| ❗  26 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

  • files_unchanged - assets/nf-core-sammyseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-sammyseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-sammyseq_logo_dark.png does not match the template

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 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 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 main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
  • pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
  • pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
  • pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
  • pipeline_todos - TODO string in main.nf: List required Conda package(s).
  • pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
  • pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
  • pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
  • pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in main.nf: List additional required output channels/values here
  • pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
  • pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
  • pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
  • pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in WorkflowSammyseq.groovy: Optionally add in-text citation tools to this list.
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-02 17:19:56

@daisymut daisymut requested a review from lucidif February 2, 2024 16:35
@daisymut daisymut marked this pull request as draft February 2, 2024 17:37
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@lucidif lucidif Awaiting requested review from lucidif

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