Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Release v1.9.0 #239

Open
wants to merge 199 commits into
base: main
Choose a base branch
from
Open

Release v1.9.0 #239

wants to merge 199 commits into from

Conversation

nvnieuwk
Copy link
Member

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

nvnieuwk and others added 30 commits September 30, 2024 14:19
@nvnieuwk
back to dev
aafc92f
@nvnieuwk
fix WES validation
d45cf25
@nvnieuwk
add --squash-ploidy to vcfeval
76ed721
@nvnieuwk
fix vcfanno input
ab6ffb1
@nvnieuwk
fix vardict flow
80cdc60
@nvnieuwk
some dbsnp fixes
4fc3da0
@nvnieuwk
some concat fixes
bee2757
@nvnieuwk
move some index creation around
053c567
@nvnieuwk
fix WGS updio
433e46d
@nvnieuwk
add a --min_callable_coverage parameter
dee3f8a
@nvnieuwk
update changelog
f248f45
@nvnieuwk
update changelog
87527a7
@nvnieuwk
fix bcftools filter
c0cb243
@nvnieuwk
create bgzipped vcfs after filtering
2d0a27f
@nvnieuwk
bump ci back to stable nf-core
aeff56b
@nvnieuwk
small typo in the actions
44bbf65
@nvnieuwk
bump read yml action
c539c6f
@nvnieuwk
fix validate snap
fbcb019
@nvnieuwk
fix vardict snap
185cf23
@nvnieuwk
fix updio test
f3d5642
@nvnieuwk
fix vardict snap
9444ea7
@nvnieuwk
fix vardict snap
599216a
@nvnieuwk
Merge pull request #204 from nf-cmgg/fix-WES-validation
1909ac9 
Fix wes validation + some general fixes
@nvnieuwk
update docs
539c12c
@nvnieuwk
re-add monochrome_logs
b7c9cf2
@nvnieuwk
Merge pull request #205 from nf-cmgg/update-docs
7f8406d 
update docs
@nvnieuwk
add skip features to nf-core.yml
a505741
@nvnieuwk
Template update for nf-core/tools version 3.0.1
0782962
@nvnieuwk
Merge branch 'TEMPLATE' into template-v3.0.1
2eace1a
@nvnieuwk
fix weird merge conflicts
5f1407b
nvnieuwk and others added 22 commits November 26, 2024 14:33
@nvnieuwk
try to fix CI
5b9102a
@nvnieuwk
try to fix CI
2ea45e0
@nvnieuwk
try to fix CI
5576499
@nvnieuwk
fix version in nf-core.yml
bd82dae
@nvnieuwk
add somalier reports to multiqc output
ea18202
@nvnieuwk
update changelog
753069f
@nvnieuwk
fix build-docs issue
6f24618
@nvnieuwk
Merge pull request #240 from nf-cmgg/multiqc-test-somalier
20e256a 
Multiqc test somalier
@nvnieuwk
Remove output suffix param (#243)
8133a49 
* remove output_suffix param

* remove output_suffix param
@nvnieuwk
add multiqc_data to output (#242)
c8882b5
@matthdsm
restore default mem for VEP
1ff7350
@nvnieuwk
update profiles
7bbf25a
@nvnieuwk
Merge pull request #245 from nf-cmgg/fix/VEP_mem
51706fd 
Fix/vep mem
@nvnieuwk
remove maxentscan from seqplorer config
2545d00
@nvnieuwk
Merge pull request #246 from nf-cmgg/update-profiles
c5dad33 
update profiles
@matthdsm
force tabix to overwrite
805dd73
@nvnieuwk
Merge pull request #247 from nf-cmgg/fix/force_tabix
c1e9bdd 
Force tabix
@nvnieuwk
add updio and automap to wes profile (#248)
523c7a9 
* add updio and automap to wes profile

* update changelog
@nvnieuwk
update vcf2db
ff80be2
@nvnieuwk
Fix config to let the tests run correctly
719004f
@nvnieuwk
Merge pull request #249 from nf-cmgg/update-vcf2db
5cb9e2c 
update vcf2db
@matthdsm
set vcf32db to process_single
e8451ab
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@matthdsm matthdsm Awaiting requested review from matthdsm

@ToonRosseel ToonRosseel Awaiting requested review from ToonRosseel

At least 1 approving review is required to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@nvnieuwk @matthdsm