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Test setup nextflow #1462

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wants to merge 61 commits into from
Closed

Test setup nextflow #1462

wants to merge 61 commits into from

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ewels
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@ewels ewels commented Dec 4, 2024

siddharthab and others added 30 commits September 3, 2024 06:16
@siddharthab
Add umicollapse as an alternative to umi-tools
fc13650 
TODO:
- [ ] Benchmark paired ends mode
- [ ] Include in multiqc
@siddharthab
Keep umitools as the default
761c56d 
Signed-off-by: Siddhartha Bagaria <[email protected]>
@LorenzoS96
add DE_analys folder
314bd76
@LorenzoS96
prettier check
72e6e2e
@siddharthab
Merge branch 'dev' into umicollapse
acd8f65
@siddharthab
update umicollapse to 1.1.0
e86e9a6
@siddharthab
update CHANGELOG
28b10ac
@LorenzoS96
change name DE folder
6d0ebe5
@LorenzoS96
modify md files
73fb0e7
@LorenzoS96
prettier check
e8d8061
@siddharthab
actually update umicollapse
e5d9d4b
@siddharthab @pinin4fjords
Apply suggestions from code review
05513ee 
Co-authored-by: Jonathan Manning <[email protected]>
@LorenzoS96 @mashehu
Update docs/usage/DEanalysis/index.md
aa35d37 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LorenzoS96 @mashehu
Update docs/usage/DEanalysis/interpretation.md
b1ec267 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LorenzoS96 @mashehu
Update docs/usage/DEanalysis/rnaseq.md
659c86b 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LorenzoS96 @mashehu
Update docs/usage/DEanalysis/rnaseq.md
f2b34d0 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LorenzoS96 @mashehu
Update docs/usage/DEanalysis/rnaseq.md
c8c7ef8 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LorenzoS96
update index.md
ae16c2c
@LorenzoS96
update images
000e228
@LorenzoS96
update interpretation
dfa8a04
@LorenzoS96
update rnaseq
aa55fe5
@LorenzoS96
update theory
f7e3c97
@LorenzoS96
update de_rstudio
dbc5260
@LorenzoS96
correct formula in theory
08efda6
@LorenzoS96
prettier check
6be4d82
@LorenzoS96
Merge pull request nf-core#1447 from LorenzoS96/dev
da5f135 
Adding differential expression analysis tutorial pages to Usage section
@pinin4fjords
Merge branch 'dev' into umicollapse
ee2dde2
@nf-core-bot
[automated] Fix code linting
b372821
@MatthiasZepper
Update tests for UMICollapse module.
88d6411
@MatthiasZepper
Update umi-tools dedup tests at well.
15116a3
pinin4fjords and others added 28 commits December 2, 2024 16:45
@pinin4fjords
Add fq/lint
dd98da7
@pinin4fjords
Add output previxes for linting
de301d2
@pinin4fjords
Tweaks
d5a14a8
@pinin4fjords
Link in new subworkflow config
380f760
@pinin4fjords
Let's skip the name validation by default, it seems to be problematic
839e21e
@pinin4fjords
Correct config
611e228
@pinin4fjords
separate linting reports by directory rather than prefix
5e1d465
@pinin4fjords
update schema
b178bc0
@pinin4fjords
Add stub to fq lint
51a7238
@pinin4fjords
update docs
25e3f9d
@pinin4fjords
update snaps
97f241a
@pinin4fjords
exclude lint reports from snapshots
ae42032
@pinin4fjords
update module/ subworkflow
83967a7
@pinin4fjords
Add CI Java fix
e69971a
@pinin4fjords
Fix java ci issue
6a6e946
@pinin4fjords
Fix subworkflow test
376296b
@pinin4fjords
Fix salmon test
2cf53ab
@pinin4fjords
Merge branch 'swf_rnaseq_prepro_lint' of https://github.com/nf-core/r…
d8649fb 
…naseq into swf_rnaseq_prepro_lint
@pinin4fjords
fix changelog and versions
7ec665d
@pinin4fjords
Update CHANGELOG.md
c0f027a
@pinin4fjords
fix version snap
803c424
@pinin4fjords
Merge branch 'swf_rnaseq_prepro_lint' of https://github.com/nf-core/r…
b8b5aa2 
…naseq into swf_rnaseq_prepro_lint
@pinin4fjords
Merge pull request nf-core#1461 from nf-core/swf_rnaseq_prepro_lint
0247f7b 
Add FASTQ linting during preprocessing
@maxulysse
Merge branch 'dev' into umicollapse
79d52f6
@MatthiasZepper
Restore truncated CHANGELOG.md with 3.0 and prior releases.
450b5b9
@nf-core-bot
[automated] Fix code linting
a2dac87
@MatthiasZepper
Merge pull request nf-core#1369 from siddharthab/umicollapse
2986385 
Add umicollapse as an alternative to umi-tools
@ewels
Make text-only change to confirm tests are broken
1a3da42
@ewels ewels closed this Dec 4, 2024
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github-actions bot commented Dec 4, 2024

This PR is against the master branch ❌

  • 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 @ewels,

It looks like this pull-request is has been made against the ewels/nf-core-rnaseq 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 ewels/nf-core-rnaseq 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!

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7 participants
@ewels @siddharthab @LorenzoS96 @pinin4fjords @nf-core-bot @MatthiasZepper @maxulysse