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Add (customisable) 'method description' MultiQC section to pipeline template #1749

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merged 24 commits into from
Sep 9, 2022
Merged

Add (customisable) 'method description' MultiQC section to pipeline template #1749

merged 24 commits into from
Sep 9, 2022

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jfy133
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@jfy133 jfy133 commented Aug 14, 2022 •
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This replaces nf-core/modules#1246 at the reques of @ewels

It adds a dynamically-created section to MultiQC, via a MultiQC YAML containing HTML, with a pipeline developer recommended text that users could copy-paste into their publications when they use a given pipeline (mainly aimed at including correct versions, the actual command used etc.).

As well as having a pipeline default (modifiable by the pipeline developer), it can also be replaced by an entirely custom text by a pipeline user with the flag --multiqc_methods_description.

This can be tested with the proof of concept on a test-pipeline here: https://github.com/jfy133/nf-core-testpipeline/tree/methods-summary

Note 1: we can improve the phrasing
Note 2: I notice the MultiQC section gets duplicated for some reason, I'm not sure why as I pretty much copy/pasted from the workflowSummary.

image

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@jfy133 jfy133 changed the base branch from master to dev August 14, 2022 06:18
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@jfy133 jfy133 mentioned this pull request Aug 14, 2022
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@jfy133 jfy133 requested a review from ewels August 14, 2022 09:21
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Update nf_core/pipeline-template/assets/methods_description_template.yml
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Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
ewels
ewels reviewed Aug 17, 2022
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Speed read-through review, haven't tested yet.

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Co-authored-by: Phil Ewels <phil@seqera.io>
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jfy133 commented Aug 17, 2022

What it looks like after committing the changes from @ewels

image

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Co-authored-by: Phil Ewels <phil@seqera.io>
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jfy133 commented Aug 23, 2022

That took longer than I would like to admit, but here we go:

image

@jfy133 jfy133 requested a review from ewels August 24, 2022 04:12
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Super nice - one minor suggestion left regarding that one bullet point, but otherwise happy to go.

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jfy133 commented Sep 9, 2022

image
image

@jfy133 jfy133 requested a review from ewels September 9, 2022 09:01
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jfy133 commented Sep 9, 2022

ugh copy and paste error ofr the screenshots, but here you go:

image

@jfy133 jfy133 merged commit 0b3441a into nf-core:dev Sep 9, 2022
@jfy133 jfy133 deleted the method-description branch September 9, 2022 11:01
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