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beatrizsavinhas wants to merge 90 commits into from
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Update dev #1

beatrizsavinhas wants to merge 90 commits into from

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@beatrizsavinhas
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@beatrizsavinhas beatrizsavinhas commented Nov 24, 2025

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/seqinspector 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).

nf-core-bot and others added 30 commits April 30, 2025 12:28
@nf-core-bot
Template update for nf-core/tools version 3.2.1
309dfbc
@nf-core-bot
Template update for nf-core/tools version 3.3.1
23d6b11
@nf-core-bot
Template update for nf-core/tools version 3.3.2
0fe7d3f
added picard tools
682576d
linting
7b44c68
@agrima2010
nf-tests
9fa9923
@agrima2010
nf tests
582938f
@agrima2010
minor changes
4576ce3
@agrima2010
minor changes
3218dc2
@agrima2010
minor changes
59e6b2b
@agrima2010
snapshots updated
01fd46a
@agrima2010
updated ss
f03a1da
@agrima2010
bwamem2 not compatible with long reads Promethion
c3d3498
@agrima2010
ss
8cdf2fd
@agrima2010
ss updated
d765d1d
@agrima2010
ss
884cb2a
@agrima2010
ss
d0141fb
@agrima2010
.nftignore
6b8c76e
@agrima2010
ss
0cfcb83
@agrima2010 @maxulysse
Update tests/.nftignore
db7395a 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@agrima2010 @maxulysse
Update tests/.nftignore
7135a9d 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@agrima2010
Test.config updates
5d129cf
@agrima2010
Merge branch 'picard_tools_dev' of https://github.com/agrima2010/seqi…
4117e63 
…nspector into picard_tools_dev
Added bwa_index parameter
c7867ab
updated process paramters for modules
b8b638f
@agrima2010
added citations and updated snapshots
16cad1b
@agrima2010
prettier and linting
f96e208
@agrima2010
linting
c11a49d
@agrima2010
linting
567a431
@agrima2010
config files updated
8a20d2d
maxulysse and others added 28 commits November 7, 2025 10:40
@maxulysse
Apply suggestions from code review
b7e66e3
@maxulysse
Apply suggestions from code review
4088174
@maxulysse
remove last trace succeeded size
5ff2807
@FranBonath
Merge pull request #133 from nf-core/nf-core-template-merge-3.4.1
e4fb3bb 
Important! Template update for nf-core/tools v3.4.1
@maxulysse
Merge branch 'dev' into bwa_index
5eeac1a
@maxulysse
Merge branch 'dev' into picard_tools_dev
f65d000
@maxulysse
fix snapshots
2b6c91d
@maxulysse
fix snapshots
0e0f236
@agrima2010
.bai files in the same folder as bam files
0fec2a2
@maxulysse
update snapshots
413fa18
@maxulysse
update modules
87b8327
@maxulysse
update snapshots once again
087c613
@maxulysse
patch fastqscreen/fastqscreen
c7142ea
@maxulysse
Merge pull request #128 from agrima2010/picard_tools_dev
da4f0fa 
Adding Picard tools for QC metrics
@maxulysse
Merge branch 'dev' into bwa_index
3aef3c6
@maxulysse
Update CHANGELOG.md
2649b29
@maxulysse
solve merge conflicts
db1437e
@nf-core-bot
Template update for nf-core/tools version 3.5.1
9214a5b
@agrima2010
removed hasta config and corrected nextflow_schema.json
7855613
@agrima2010
nextflow_schema.json
b7cbd8e
@agrima2010
nextflow.config
457e19b
@agrima2010
removed channel output of BAM from seqinspector.nf
df0f9c0
@agrima2010
bwa_index added to nextflow.config
16f508a
@agrima2010 @maxulysse
Update nextflow_schema.json
e8ac39a 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@agrima2010
Merge pull request #132 from agrima2010/bwa_index
f3fb6f8 
Added optional Bwa index parameter to skip bwamem2 index for a faster output
@maxulysse
Merge branch 'dev' into nf-core-template-merge-3.5.1
d4b1e9f
@maxulysse
fix multiqc modules install
9a462c2
@maxulysse
Merge pull request #144 from nf-core/nf-core-template-merge-3.5.1
fce9278 
Important! Template update for nf-core/tools v3.5.1
@beatrizsavinhas
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beatrizsavinhas commented Nov 24, 2025

Incorrect action. Merging remote dev into dev instead.

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5 participants

@beatrizsavinhas @nf-core-bot @agrima2010 @maxulysse @FranBonath