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Add pipeline functionality #21

Merged
merged 18 commits into from
Jun 4, 2023
Merged

Add pipeline functionality #21

merged 18 commits into from
Jun 4, 2023

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christopher-mohr
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Draft PR for the Nanostring pipeline functionality. This adds the following functionality

  • input check
  • NACHO QC
  • NACHO normalization
  • postprocessing (annotated count tables, WIP)
  • adding content to MultiQC

Known issues:

  • NACHO PCA plot generation fails (commented out)
  • Mulled container seems to be missing pandoc
  • Postprocessing script needs to be further adapted

@apeltzer apeltzer marked this pull request as ready for review June 4, 2023 14:57
@apeltzer apeltzer merged commit c545b4d into nf-core:dev Jun 4, 2023
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github-actions bot commented Jun 4, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3fb26ab

+| ✅ 158 tests passed       |+
!| ❗  12 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 nextflow.config: Specify your pipeline's command line flags
  • 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 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 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 prefered 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-02 15:39:32

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@apeltzer apeltzer apeltzer approved these changes

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@christopher-mohr @apeltzer