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Nf core template merge 2.12 #96

Merged
merged 21 commits into from
Feb 2, 2024
Merged

Nf core template merge 2.12 #96

merged 21 commits into from
Feb 2, 2024

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MariekeVromman
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@MariekeVromman MariekeVromman commented Feb 1, 2024 •
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Hi, this is the first time I'm trying to merge an automated PR, so I was unsure about some things. I tried following the nf-core docs on "Merging automated PRs".

Can some more experienced people double-check to see what I missed?
As I'm new to this, feel free to delete this PR if it's more trouble trying to fix it, than just starting from scratch, no problem!

These are the changes I made:

  • whenever it was a 'version update', I approved the change

for example: .github/workflows/awsfulltest.yml

  • some more elaborate updates of 'standard' files I also approved the change

.github/workflows/fix-linting.yml
.github/workflows/linting.yml
modules/nf-core/fastqc/tests/main.nf.test
assets/nf-core-circrna_logo_light.png

  • some files I kept the original nf-core/circrna dev code, as the proposed PR changes seemed to remove specific pipeline stuff (and often replace it with nothing), so it made more sense to me to keep the original

CITATIONS.md
conf/modules.config
main.nf
nextflow_schema.json

  • sometimes I made a combination of both. I guess these are the files that need the most proof-reading

README.md
docs/output.md
docs/usage.md
modules.json
nextflow.config

  • I'm not sure about these two files where args is added. For now, I did not follow the update. Could someone check if this is correct?

lib/WorkflowMain.groovy
main.nf

  • I'm also not sure about this one. It suggested to remove the params.species check, but I assume it's useful to keep it? So I kept it

lib/WorkflowMain.groovy

  • and about this one, which tried to change the INPUT_CHECK process
    line 116 in workflows/circrna.nf

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github-actions bot commented Feb 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e0a0123

+| ✅ 192 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • system_exit - System.exit in circrna.nf: System.exit(1) [line 43]

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-02 08:35:09

@maxulysse maxulysse changed the base branch from nf-core-template-merge-2.12 to dev February 1, 2024 12:44
@maxulysse
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I changed the target to dev

@nictru
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nictru commented Feb 1, 2024 •
edited by MariekeVromman
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So there are three things that should be adressed here I think:

  • Linting: There are some inconsistencies between nextflow.schema (the file that is relevant for the documentation) and nextflow.config (the file that is used for the pipeline). They should be pretty easy to fix
  • Pipeline execution: There is some problem in the pipeline, which makes it not executable. Could you try running it with the test configuration, to make sure everything works properly?
  • Documentation: Sometimes it is a bit hard to keep track of all the changes that are made, so once the other problems are sorted out, we can check if something got messed up in documentation

maxulysse
maxulysse reviewed Feb 1, 2024
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mashehu
mashehu approved these changes Feb 2, 2024
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MariekeVromman and others added 2 commits February 2, 2024 09:31
@MariekeVromman @mashehu
fix typo in docs/output.md
dbcbf1a 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@MariekeVromman
remove redundant output declaration
e0a0123
@MariekeVromman MariekeVromman merged commit 6cdab70 into nf-core:dev Feb 2, 2024
4 checks passed
@MariekeVromman MariekeVromman deleted the nf-core-template-merge-2.12 branch February 6, 2024 10:48
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@maxulysse maxulysse maxulysse left review comments

@mashehu mashehu mashehu approved these changes

@nictru nictru nictru approved these changes

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@MariekeVromman @maxulysse @nictru @mashehu @nf-core-bot