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Merged
merged 165 commits into from
May 8, 2025
Merged

First release 🔝 #6

merged 165 commits into from
May 8, 2025

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jkh00
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@jkh00 jkh00 commented Apr 10, 2025 •
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  • Check the pipeline follows nf-core guidelines.
  • All continuous-integration tests on the dev branch should be passing
  • Check that there are no outstanding issues that need to be addressed, especially bug reports.
  • Finalize the description of the pipeline in the GitHub repository and ensure that you remove any “under development” labels in the description. This wording will be used when a new pipeline gets announced on our socials (Bluesky and Mastodon).
  • Check that the full-size tests have successfully completed within the dev branch
  • Bump the version number of the dev branch to a release version
  • Update CHANGELOG.md
  • PR approved by two reviewers
  • (First release only) Ask a core team member to activate the Zenodo functionality for this repository, which will be used to generate a DOI.
  • AWS tests passed

ra25wog and others added 30 commits January 15, 2025 10:33
added modules
fc8c63d
updated module.config and main.nf of workflows and subworkflows
e51b598
updated subworkflows, mostly how inputs are defined
5dd6aa0
updated ont workflow
38b5228
updated ont workflow and publish directories
31c3292
updated pacbio workflow
31f05b9
correcting inputs
b5c8626
next:resolve params.model = some_value weird issue
bee93b9
bunch of updates
d1ce6ed
fixing 99 problems
c4e13f7
update readme
da79d55
update readme
960d96e
update files
088156c
add again bunch of stuff
3869147
update test config
d52bb35
linting test passed
3e6e87f
added workflow figure
6b4473b
@jkh00
Update README.md
1f185a8
@jkh00
Add files via upload
bdc9433
@jkh00
Add files via upload
1642ea3
@jkh00
Update README.md
d5f2b4d
update readme
aa7016d
update test.config
3c611eb
update readme
7e2b232
updates
16fa0c7
changed script
8215db8
@jkh00
Merge pull request #1 from jkh00/dev
830d5d0 
update codes
resolved caching issue
caf6ae6
updates
186ab07
@jkh00
Merge pull request #3 from jkh00/dev
b1f2b55 
resolved caching issue
ra25wog and others added 29 commits April 26, 2025 20:22
update resource for full test
a35b430
@jkh00
Merge pull request #37 from nf-core/fix4firstPR
36b68c0 
update resource for full test
update resource for full test
28d0d80
@jkh00
Merge pull request #38 from nf-core/fix4firstPR
f48b21e 
update resource for full test
@nf-core-bot
Template update for nf-core/tools version 3.2.1
528d0e8
Merge branch 'dev' into nf-core-template-merge-3.2.1
414626a
@jkh00
Merge pull request #39 from nf-core/nf-core-template-merge-3.2.1
c6264c2 
Important! Template update for nf-core/tools v3.2.1
disable trimming part in aws full
8499325
@jkh00
Merge pull request #42 from nf-core/fix4firstPR2
c0a4fba 
disable trimming part in aws full test
updated fastqc
1fe5b61
@jkh00
Merge pull request #43 from nf-core/fix4firstPR2
a6a38c3 
updated fastqc
updated resources for full test
833b6fd
@jkh00
Merge pull request #44 from nf-core/fix4firstPR2
865f5f3 
updated resources for full test
updated dorado version
792a369
@jkh00
Merge pull request #45 from nf-core/fix4firstPR2
651ce97 
updated dorado version
fix container not found issue
8fc4047
@jkh00
Merge pull request #46 from nf-core/fix4firstPR2
630bec9 
fix container not found issue
added samtools reset for dorado workflow
ed1237c
update minimap2 module
831c2a4
@jkh00
Merge pull request #47 from nf-core/fix4firstPR2
45644d7 
Fix4first pr2
update README
59bb91b
@jkh00
Merge pull request #48 from nf-core/fix4firstPR2
0eaec0a 
update README
include samtools reset in ONT trim_repair workflow
63324cb
improved condition calling, prevent double reset
9875c9b
changed required resources for pbmm2 in aws test
436fc30
@jkh00
Merge pull request #49 from nf-core/fix4firstPR2
338f6c4 
include samtools reset in ONT trim_repair workflow
updated output.md and release tag
8663dc3
solved minor caching issue
65d369d
@jkh00
Merge pull request #50 from nf-core/fix4firstPR2
0ecf817 
Fix4first pr2
@jkh00 jkh00 merged commit 597317b into master May 8, 2025
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@mirpedrol mirpedrol mirpedrol approved these changes

@fellen31 fellen31 fellen31 approved these changes

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@jkh00 @mashehu @mirpedrol @fellen31 @nf-core-bot