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Merged
itrujnara merged 267 commits into from
Oct 21, 2025
Merged

Release 1.1.0 #89

itrujnara merged 267 commits into from
Oct 21, 2025

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@itrujnara
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@itrujnara itrujnara commented Mar 28, 2025

This is the pull request for release 1.1.0. See the changelog for changes.

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/reportho 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).

itrujnara and others added 30 commits October 10, 2024 09:46
@itrujnara
Make linter happier
deebdd2
@itrujnara
Make linter happy about subworkflows
eb14c59
@itrujnara
Change Nextflow version for tests again
f431750
@itrujnara
Update test configs to use resourceLimits
85c9529
@itrujnara
Put resource limits where they should be
d2858b6
@itrujnara @maxulysse
Update conf/test_full.config
e1a6d24 
Co-authored-by: Maxime U Garcia <[email protected]>
@itrujnara
Add nf-schema utils to modules.json
a0dd1d7
@itrujnara
Change resource limits in custom tests to match defaults
f102a12
@nf-core-bot
Template update for nf-core/tools version 3.0.2
eb270c1
@itrujnara
Merge pull request #61 from itrujnara/merge-template-3-0-1
98a77b6 
Merge template version 3.0.1
@itrujnara
Template update for nf-core/tools version 3.0.1
33d98d2
@itrujnara
Merge template version 3.0.2
9ffb7ee
@itrujnara
Correct version of changelog
4afc381
@itrujnara
Make prettier happy
a9e84e3
@itrujnara
Make prettier happy again
d711525
@itrujnara @mashehu
Update .github/CONTRIBUTING.md
2d153fe 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@itrujnara @maxulysse
Update CITATIONS.md
b0f8e7d 
Co-authored-by: Maxime U Garcia <[email protected]>
@itrujnara
Merge pull request #63 from itrujnara/dev
43b7529 
Merge template version 3.0.2
@itrujnara
Split the orthologs subworkflow in preparation for new modules
26bada9
@itrujnara
Start adding new sequence fetch scripts
751f07b
@itrujnara
Add utilities for list-to-file writing and sequence information
6e390db
@itrujnara
Tweak OMA and Uniprot sequence fetching to the new design
3599094
@itrujnara
Rewrite Ensembl fetching to match the new format
0ea28c6
@itrujnara
Add refseq fetch script
48093f8
@itrujnara
Change sequence fetch module to OMA specific
6a5b74f
@itrujnara
Add nf-core cat/cat module
52f080a
@itrujnara
Add module to fetch ensembl idmap
3cea4d2
@itrujnara
Add module to split IDs by format
dcb7306
@itrujnara
Add module to fetch ensembl sequences
309c46f
@itrujnara
Add module to fetch RefSeq sequences
85925d9
@itrujnara
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itrujnara commented Jul 3, 2025

@MeriamOs @atrull314 I have merged the 3.3.1 template and fixed the resulting CI issues. There is 1 remaining CI failure, but you can re-review the PR at your convenience. Thank you for the help.

@itrujnara itrujnara merged commit 9e8ae5a into master Oct 21, 2025
54 of 61 checks passed
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@atrull314 atrull314 atrull314 approved these changes

@MeriamOs MeriamOs MeriamOs approved these changes

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@itrujnara @atrull314 @MeriamOs @nf-core-bot @JoseEspinosa @alessiovignoli