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Dev PR for Release 1.3 #146

Merged
merged 131 commits into from
Apr 8, 2024
Merged

Dev PR for Release 1.3 #146

merged 131 commits into from
Apr 8, 2024

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ypriverol
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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/quantms 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).

jspaezp and others added 30 commits September 15, 2023 15:15
@jspaezp
stuff
ec28eab
@ypriverol
Merge pull request #2 from bigbio/dev
5508231 
major changes
@daichengxin
Merge pull request #6 from nf-core/dev
e41cc4c 
Dev
@daichengxin
Merge pull request #7 from nf-core/dev
fc19df9 
Dev
@daichengxin
Merge pull request #10 from bigbio/dev
445e2f8 
u
@nf-core-bot
Template update for nf-core/tools version 2.11
c2b4ca4
@nf-core-bot
Template update for nf-core/tools version 2.11.1
c1de156
@daichengxin
remove multiqc warning
7dc473a
@daichengxin
Merge branch 'dev' into nf-template
80b18d3
@daichengxin
Update CHANGELOG.md
6b73ded
@daichengxin
Update CHANGELOG.md
371c9d6
@daichengxin
remove fastqc
23d4e2f
@daichengxin
Merge pull request #11 from daichengxin/nf-template
788bd79 
Template update for nf-core/tools version 2.11
@daichengxin
fixed sage cache
2d4b836
@daichengxin
Merge branch 'dev' of https://github.com/daichengxin/quantms into dev
a7f6444
@daichengxin
fixed regular match
b3b47e2
@daichengxin
Update diann_convert.py
898f721
@daichengxin
fixed schema json
e80ba58
@ypriverol
Merge pull request #331 from daichengxin/dev
d770c74 
fixed multiple bugs and nf-template
@jspaezp
first branch commit
b1cee70
@jspaezp
added params
0bbfaaf
@jspaezp
fixed unused reference
0c12076
@jspaezp
trailing comma
2ab21a3
@jspaezp
stuff
4217740
@jspaezp
added node modules to gitignore
4b0badc
@jspaezp
merged branch onto bigbio dev
8237a29
@jspaezp
rolled back sdrf parsing
94e6d16
@jspaezp
Merge branch 'dev' into bb_feature/skip_prelim
66a0f7a
@jspaezp
removed accidental file
639e507
@daichengxin
Merge pull request #12 from TalusBio/bb_feature/skip_prelim
3c80318 
Bb feature/skip prelim
@ypriverol ypriverol linked an issue Mar 21, 2024 that may be closed by this pull request
URGENT: pin nf-validation version #144
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@ypriverol
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Ping @jpfeuffer

@ypriverol @jpfeuffer
Update modules/local/diann_preliminary_analysis/main.nf
a7205a4 
Co-authored-by: Julianus Pfeuffer <julianus.pfeuffer@pfizer.com>
jpfeuffer
jpfeuffer reviewed Mar 22, 2024
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See comments. Rest looks good

@ypriverol
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@jpfeuffer @daichengxin changes done. Please review.

@ypriverol ypriverol merged commit 72e2b6a into nf-core:dev Apr 8, 2024
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@daichengxin daichengxin daichengxin approved these changes

@jpfeuffer jpfeuffer Awaiting requested review from jpfeuffer

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URGENT: pin nf-validation version
5 participants
@ypriverol @jpfeuffer @daichengxin @jspaezp @nf-core-bot