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v2.7.0 release #336

Merged
merged 175 commits into from
Jun 25, 2024
Merged

v2.7.0 release #336

merged 175 commits into from
Jun 25, 2024

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grst
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@grst grst commented Jun 3, 2024

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/scrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

fmalmeida and others added 30 commits November 7, 2023 11:31
@fmalmeida
Add cellranger multi testing assets
94397e5
@fmalmeida
allow cellrangermulti option
e6a54bb
@fmalmeida
include cellrangermulti testing conf/profile
ae20b9e
@fmalmeida
allow cellrangermulti option
5863d2c
@fmalmeida
fix example samplesheet
631a980
@fmalmeida
fixed samplesheet for cellranger multi
70fff60
@fmalmeida
don't get cellrangemulti metadata if not needed
f97e430
@fmalmeida
fix check_samplesheet script to be more generic
ff66e97
@fmalmeida
update input_check for cellranger multi
0af2761
@fmalmeida
avoid renaming sample ids in input check
8e7d436
@fmalmeida
generate a parsed input channel for cellrangermulti sub-workflow
97281aa
@fmalmeida
defined cellrangemulti sub-workflow and parsed input channel for exec…
8b19f48 
…ution
@fmalmeida
included gex (normal) reference building and updated cellranger modules
6f494fe
@fmalmeida
include mkvdjref
215226b
@fmalmeida
refactored sample mapping
7b86f80
@fmalmeida
finally cellranger multi running, with errors, but now can be debugged
e6dc3b2
@fmalmeida
not finding samples in data directory
7c66115
@fmalmeida
saving quick changes for shifting development workspace
abb0e3c
include option for unzipping reference files
5e27a4c
@fmalmeida
First successfull run of cellranger multi with renaming module
e00a78d
@fmalmeida
add whiteline
ead6462
Testing github traffic
ab4425e
Remove file used for testing
2cfb148
input dataset parsing refactored and fixed
4c275b4
include cellrangermulti outputs in mqc channel
a8d2702
include option for cellrangermulti in mtx conversion modules
0d8be69
add files filter for cellranger multi outputs
4d75c83
include cellranger multi outputs to mtx conversion subworkflow
e4e37b5
update changelog
132e247
remove unused file
0ec7019
grst and others added 20 commits May 15, 2024 11:33
@grst
Update output documentation
c95b11c
@grst
Update nextflow_schema.json
f4304ad
@fmalmeida
remove gex_barcode_sample_assignment parameter
03a38cd
@fmalmeida
add note
e22f986
@grst
Update nextflow schema documentation
0d0275e
@grst
Revert "remove gex_barcode_sample_assignment parameter"
882812c 
This reverts commit 03a38cd.
@grst
Revert "add note"
708c903 
This reverts commit e22f986.
@maxulysse
Merge branch 'dev' into nf-core-template-merge-2.14.1
77b269f
@maxulysse
Update modules.config
75f56b2
@maxulysse
Merge pull request #328 from nf-core/nf-core-template-merge-2.14.1
af39884 
Important! Template update for nf-core/tools v2.14.1
@maxulysse
Merge branch 'dev' into 247-support-for-10x-ffpe-scrna
b3afdb7
@maxulysse
update file
d497ca8
@maxulysse
update file better
4d9f17e
@maxulysse
Merge pull request #276 from nf-core/247-support-for-10x-ffpe-scrna
7286aa6 
Adding cellrangermulti subworkflow
@nictru
Add check_max to AlevinQC time limit
da41396
@grst
Merge pull request #335 from nf-core/fix-334
a4efbde 
Add `check_max` to AlevinQC time limit
@grst
Merge branch 'dev' into bump-version
42b86c0
@grst
Update CHANGELOG
53977b3
@grst
Bump version to 2.7.0
3b05cae
@grst
Merge pull request #325 from nf-core/bump-version
411d5fe 
Bump version for v2.7 release
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github-actions bot commented Jun 3, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 64a3382

+| ✅ 203 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.7.0
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-04 09:34:15

@grst grst requested review from fmalmeida and apeltzer June 3, 2024 11:49
fmalmeida
fmalmeida reviewed Jun 3, 2024
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workflows/scrnaseq.nf

main:

protocol_config = Utils.getProtocol(workflow, log, params.aligner, params.protocol)
if (protocol_config['protocol'] == 'auto' && params.aligner != "cellranger") {
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Based on the protocols.json I think cellrangerarc must also be part of this check.

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Maybe a contains should be fine to include both cases ...? However being explicit here is also maybe a good idea, so that its obvious what applies here.

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@fmalmeida fmalmeida Jun 4, 2024 •
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think a params.aligner in [ 'cellranger', 'cellrangerarc' ] might make it explicit enough

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added a patch for that: #337

apeltzer
apeltzer approved these changes Jun 3, 2024
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Looks good to me.

fmalmeida
fmalmeida approved these changes Jun 5, 2024
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Looks good.
Once release, efforts should be made/focused on:

  • Simplifying this the samplesheet checker on: subworkflows/local/utils_nfcore_scrnaseq_pipeline/main.nf
  • Adding a proper cellranger-arc testing profile and nf-test

@grst grst merged commit c8f02f5 into master Jun 25, 2024
27 of 28 checks passed
@vd4mmind vd4mmind mentioned this pull request Jul 1, 2024
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@apeltzer apeltzer apeltzer approved these changes

@fmalmeida fmalmeida fmalmeida approved these changes

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6 participants
@grst @apeltzer @fmalmeida @nf-core-bot @maxulysse @nictru