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updating name of process in config #47

Merged
merged 1 commit into from
Oct 31, 2023
Merged

updating name of process in config #47

merged 1 commit into from
Oct 31, 2023

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jemten
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@jemten jemten commented Oct 30, 2023

The name of the process that generates the sample annotation file is different in modules.config file compared to the what it is called in the analyse transcripts subworkflow.

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
  • 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 Oct 30, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e14b76f

+| ✅ 130 tests passed       |+
#| ❔ 258 tests were ignored |#
!| ❗  16 tests had warnings |!

❗ 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 README.md: Add bibliography of tools and data used in your pipeline
  • 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 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
  • 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 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 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 tomte.nf: change this to use the plugin nf-validation
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/genomic-medicine-sweden/tomte/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/nf-core/tomte/master/nextflow_schema.json

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-30 16:21:40

@jemten jemten marked this pull request as ready for review October 31, 2023 07:48
@jemten jemten requested a review from Lucpen as a code owner October 31, 2023 07:48
Lucpen
Lucpen approved these changes Oct 31, 2023
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LGTM!

@jemten jemten merged commit 8a96f05 into master Oct 31, 2023
7 checks passed
@jemten jemten deleted the fix_process_name_in_conf branch October 31, 2023 10:17
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@Lucpen Lucpen Lucpen approved these changes

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