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Merged
lescai merged 14 commits into from
May 10, 2022
Merged

Modules installing to prepare workflow submission #2

lescai merged 14 commits into from
May 10, 2022

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@carpanz
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@carpanz carpanz commented May 9, 2022

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/hgtseq 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).

@carpanz carpanz requested a review from lescai May 9, 2022 17:28
lescai
lescai requested changes May 10, 2022
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I world recommend removing the local ranalysis module from this PR, so this is only about installing nf-core tested modules and we can focus one of the following PRs to proper code review of each local module(s)

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carpanz commented May 10, 2022

Done! @lescai

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github-actions bot commented May 10, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a22b127

+| ✅ 146 tests passed       |+
!| ❗  20 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Write a 1-2 sentence summary of what data the pipeline is for and what it does
  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 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
  • 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 hgtseq.nf: Add all file path parameters for the pipeline to the list below

✅ Tests passed:

Run details

  • nf-core/tools version 2.3.2
  • Run at 2022-05-10 17:25:09

lescai
lescai requested changes May 10, 2022
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json files (modules.json failing Prettier) seem to need a new line character at the end of the file to be valid

@carpanz @lescai
Update modules.json
a22b127 
Co-authored-by: Francesco L <[email protected]>
lescai
lescai approved these changes May 10, 2022
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LGTM now. I will skip last test until we get subworkflows we can actually test

@lescai lescai merged commit eee7309 into nf-core:dev May 10, 2022
lescai pushed a commit that referenced this pull request May 12, 2023
@carpanz
Merge pull request #2 from carpanz/modules_update
98c1e78 
forgot to update samtools version in local module and CHANGELOG
lescai added a commit that referenced this pull request Nov 14, 2025
@lescai
Merge pull request #2 from lescai/codex/fix-nullpointerexception-in-p…
5192da3 
…ipeline

Fix SORTBAM join to avoid Nextflow NullPointerException
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@carpanz @lescai