This replaces https://github.com/nf-core/modules/pull/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.

PR checklist

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

Aug 14 '22 06:08 jfy133

This PR is against the `master` branch :x:

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the jfy133/nf-core-tools master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the jfy133/nf-core-tools dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

Aug 14 '22 06:08 github-actions[bot]

Codecov Report

Merging #1749 (710044a) into dev (d404374) will increase coverage by 0.02%. The diff coverage is 68.18%.

@@            Coverage Diff             @@
##              dev    #1749      +/-   ##
==========================================
+ Coverage   69.22%   69.25%   +0.02%     
==========================================
  Files          59       59              
  Lines        7142     7148       +6     
==========================================
+ Hits         4944     4950       +6     
  Misses       2198     2198

Impacted Files	Coverage Δ
nf_core/lint/files_exist.py	`78.00% <ø> (ø)`
nf_core/lint/files_unchanged.py	`72.61% <ø> (ø)`
nf_core/modules/modules_json.py	`74.65% <ø> (ø)`
nf_core/modules/update.py	`75.37% <0.00%> (ø)`
nf_core/schema.py	`76.28% <0.00%> (ø)`
nf_core/create.py	`62.35% <22.22%> (-1.07%)`	:arrow_down:
nf_core/modules/modules_repo.py	`84.21% <66.66%> (+1.35%)`	:arrow_up:
nf_core/__main__.py	`53.50% <100.00%> (+0.72%)`	:arrow_up:
nf_core/lint/__init__.py	`74.18% <100.00%> (+0.10%)`	:arrow_up:
nf_core/modules/lint/__init__.py	`83.06% <100.00%> (+0.59%)`	:arrow_up:
... and 3 more