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Add CHM13 igenomes reference #64

Merged
merged 8 commits into from Sep 22, 2022
Merged

Add CHM13 igenomes reference #64

merged 8 commits into from Sep 22, 2022

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edmundmiller
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@edmundmiller edmundmiller commented Sep 17, 2022 •
edited

PR checklist

Adds igenomes config for CHM13. Also fixes a bug with the bwamem2 index

  • 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/nascent 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).

@edmundmiller edmundmiller self-assigned this Sep 17, 2022
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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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github-actions bot commented Sep 17, 2022 •
edited

nf-core lint overall result: Failed ❌

Posted for pipeline commit f52ac20

+| ✅ 152 tests passed       |+
!| ❗  23 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/workflows/linting.yml does not match the template

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.1.0'
  • 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: Update the example "typical command" below used to run the pipeline
  • 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 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 nascent.nf: Add all file path parameters for the pipeline to the list below
  • 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 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_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
  • schema_description - Ungrouped param in schema: save_reference
  • schema_description - Ungrouped param in schema: aligner
  • schema_description - Ungrouped param in schema: transcript_identification
  • schema_description - Ungrouped param in schema: with_tuning
  • schema_description - Ungrouped param in schema: gtf
  • schema_description - Ungrouped param in schema: gff
  • schema_description - Ungrouped param in schema: gene_bed
  • schema_description - Ungrouped param in schema: skip_alignment

✅ Tests passed:

Run details

  • nf-core/tools version 2.5.1
  • Run at 2022-09-19 17:14:17

@edmundmiller edmundmiller added this to the v2.0.0 milestone Sep 19, 2022
@jfy133
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jfy133 commented Sep 21, 2022 •
edited

Isn't bwamem_index2 default missing from nextflow. Config

Edit: or the the bug is it was already added and schema missed (sorry looking from my phone)

@edmundmiller
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Isn't bwamem_index2 default missing from nextflow. Config

It's actually defined in main.nf but then it wasn't in the schema! I just followed what they did in sarek.

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jfy133 commented Sep 21, 2022

Hmm, @nf-core/sarek is it correct you have params in schema that isn't in nextflow.config (i.e. do you really specify defaults in the main.nf?)?

@drpatelh
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Bunch of lint tests failing?

@edmundmiller
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Bunch of lint tests failing?

See #61 😬

@edmundmiller edmundmiller merged commit 3c81073 into dev Sep 22, 2022
@edmundmiller edmundmiller deleted the CHM13 branch September 22, 2022 15:15
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@drpatelh drpatelh drpatelh approved these changes

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