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Add quality control metrics as MultiQC custom content #88

Merged
merged 7 commits into from
Oct 11, 2024
Merged

Add quality control metrics as MultiQC custom content #88

merged 7 commits into from
Oct 11, 2024

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fasterius
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This PR adds the quality controls metrics from the report to MultiQC as custom content. Additionally, the way the metrics are presented in the report are harmonised to be shown in a more similar manner.

This is related to #40.

@fasterius
Add MultiQC custom content for QC metrics
b998f6a
@fasterius
Clarify subworkflow outputs channel names
363790c
@fasterius
Also publish QC metrics file
c384af7
@fasterius
Add patch to MultiQC for multi-platform image
0374c7f
@fasterius
Update quality control MultiQC section description
7123af0
@fasterius
Update and harmonise QC filtering numbers
ba22252 
Update and harmonise the QC filtering numbers, which had slightly
different wording and counting of the number of spots/genes that were
filtered at each step. Now they follow the format of `Removed X
[spots/genes] with Y [feature cut-off]` or similar. Each filtering step
still depends on the former step.
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github-actions bot commented Sep 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ae0a9a8

+| ✅ 181 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   3 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: 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 awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: assets/nf-core-spatialvi_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_dark.png
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-13 07:12:50

cavenel
cavenel approved these changes Oct 11, 2024
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All good!

@cavenel cavenel merged commit a4abaad into dev Oct 11, 2024
8 checks passed
@fasterius fasterius deleted the multiqc-custom-content branch October 11, 2024 13:53
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@fasterius @cavenel