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Some parameter changes, added qbic credits #254

Merged
merged 12 commits into from
Mar 22, 2024
Merged

Some parameter changes, added qbic credits #254

merged 12 commits into from
Mar 22, 2024

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WackerO
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@WackerO WackerO commented Mar 20, 2024

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
  • If necessary, also make a PR on the nf-core/differentialabundance branch on the nf-core/test-datasets repository.
  • 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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WackerO commented Mar 20, 2024

For the future: Should there be two separate sets of params features_id/name_col? ATM, these params are used both for the counts file and the GTF; I think the two files should be treated separately, no?

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github-actions bot commented Mar 20, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0854d3f

+| ✅ 272 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-22 13:30:18

@WackerO WackerO mentioned this pull request Mar 20, 2024
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pinin4fjords
pinin4fjords requested changes Mar 21, 2024
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Nice work on the config ID tweaks, but I don't think moving options out of the respective sections is helpful for someone looking for those options.

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WackerO and others added 7 commits March 21, 2024 12:29
@WackerO @pinin4fjords
Update README.md
37fa90a 
Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
@WackerO @pinin4fjords
Update conf/modules.config
a64c11a 
Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
@WackerO @pinin4fjords
Update conf/modules.config
0c352eb 
Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
@WackerO @pinin4fjords
Update conf/modules.config
ba94655 
Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
@WackerO
Returned advanced options to their sections, removed default for obse…
1f15666 
…rvations_name_col
@WackerO
linting
8fa83dd
@WackerO
removed advanced options key from schema, re-added example of observa…
82cba18 
…tions_name_col
pinin4fjords
pinin4fjords approved these changes Mar 21, 2024
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Looking pretty good, only a minor suggestion

nextflow_schema.json
@@ -119,7 +119,6 @@
},
"observations_name_col": {
"type": "string",
"default": "sample",
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Maybe mention in the description that we will now default to the same column as the ID?

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done!

@WackerO WackerO merged commit 2972621 into nf-core:dev Mar 22, 2024
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@WackerO WackerO deleted the simplify branch March 22, 2024 14:45
@WackerO WackerO mentioned this pull request Jul 4, 2024
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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