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Dev -> master for 3.13.2 release #1128

Merged
merged 36 commits into from
Nov 21, 2023
Merged

Dev -> master for 3.13.2 release #1128

merged 36 commits into from
Nov 21, 2023

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pinin4fjords
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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/rnaseq 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).

pinin4fjords and others added 30 commits November 20, 2023 12:13
@pinin4fjords
[skip ci] overhaul tximport.r
5b99b9b
@pinin4fjords
Fix formatting etc in tximport script
5f1826d
@pinin4fjords
update workflow files for new tximport script
489bcb4
@pinin4fjords
appease eclint
a9a831c
@pinin4fjords
appease eclint
b706662
@pinin4fjords
Ensure pseudoaligner is set if pseudoalignment is not skipped
7533e9f
@pinin4fjords
Update changelog
10d8086
@pinin4fjords
restore script executability
6bc74b6
@pinin4fjords
correct typo
3e30c26
@pinin4fjords
Fix tower yml
736bffa
@pinin4fjords
[skip ci] bump version in config
279fd12
@pinin4fjords
Move release to minor version, include tximport PR
8ed06f3
@pinin4fjords
[skip ci] Back to patch release
8615a86
@rhr-cosyne
fix: remove GTF_FILTER.out.versions
249c2a9
@RHReynolds
docs: update CHANGELOG
5c50f7d
@RHReynolds
docs: move update to dev
1398f5c
@pinin4fjords
Fix error message
0a675cf
@pinin4fjords
Fix CHANGELOG.md
317e2e0
@nf-core-bot
[automated] Fix linting with Prettier
5e42930
@pinin4fjords
Merge pull request #1126 from RHReynolds/fix-skip-gtf
da99418 
Fix pipeline failure when transcript_fasta not provided and skip_gtf_filter is set to TRUE
@pinin4fjords
Merge branch 'dev' into ensure_notnull_pseudo
05c4918
@nf-core-bot
[automated] Fix linting with Prettier
e1a5cca
@pinin4fjords
Merge branch 'ensure_notnull_pseudo' of github.com:nf-core/rnaseq int…
0f6fec6 
…o ensure_notnull_pseudo
@pinin4fjords
Add credits
89666a4
@MatthiasZepper
Enlarge the sampling range for column determination in FilterGTF script.
4e47864
@MatthiasZepper
Prettier on Markdown documents.
0b2da65
@MatthiasZepper
New version of Prettier, new changes to Markdown. Love it....not.
6b85d1e
@pinin4fjords
Update CHANGELOG.md
9250c4c
@pinin4fjords
Merge pull request #1127 from MatthiasZepper/FilterGTF_enlage_sample
76464e4 
Enlarge the sampling range for column determination in FilterGTF script.
@pinin4fjords
Merge branch 'dev' into ensure_notnull_pseudo
065c63a
@pinin4fjords pinin4fjords changed the title Dev -> master for 3.13.1 release Dev -> master for 3.13.2 release Nov 21, 2023
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github-actions bot commented Nov 21, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b7480f7

+| ✅ 144 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 3.13.2
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-21 10:43:26

drpatelh
drpatelh approved these changes Nov 21, 2023
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Thank you 🙏🏽 I have reviewed the smaller PRs already and all looks great.

@pinin4fjords
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Thanks @maxulysse @drpatelh !

@pinin4fjords pinin4fjords merged commit a10f41a into master Nov 21, 2023
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@drpatelh drpatelh drpatelh approved these changes

@maxulysse maxulysse maxulysse approved these changes

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7 participants
@pinin4fjords @maxulysse @drpatelh @rhr-cosyne @RHReynolds @nf-core-bot @MatthiasZepper