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

Candidate release 3.3.0 #1199

Merged
merged 720 commits into from
Sep 13, 2023
Merged

Candidate release 3.3.0 #1199

merged 720 commits into from
Sep 13, 2023

Conversation

maxulysse
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
  • If necessary, also make a PR on the nf-core/sarek 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).

robsyme and others added 30 commits August 15, 2023 07:28
@robsyme @maxulysse
Update nextflow_schema.json
43138f0 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
@robsyme @maxulysse
Update nextflow_schema.json
f9fd774 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
@FriederikeHanssen
Merge branch 'dev' into refactor_hc
8c4ca97
@maxulysse
Merge branch 'dev' into more_manual_tests
cc94ce2
@maxulysse
Merge branch 'dev' into master
0ba4cf5
@nf-core-bot
[automated] Fix linting with Prettier
0ed3a6e
@maxulysse
Update CHANGELOG.md
7c28d96
@maxulysse
Merge pull request #1166 from ATpoint/master
57a8026 
note on '--tools' in Quickstart
@maxulysse
Merge pull request #930 from maxulysse/more_manual_tests
b01d759 
Add more manual tests
@asp8200
Update modules
2f30bdf
@asp8200
Add required input channels for bcftools_stats
0dce1c0
@asp8200
Trying to fix call to SENTIEON_BWAMEM
2e02a1c
@FriederikeHanssen
Merge pull request #1177 from FriederikeHanssen/nf_val
38c57e6 
Status inference update
@asp8200
Trying to fix call to SENTIEON_BWAMEM
3c69795
@FriederikeHanssen
remove docker tag
a73b0b3
@FriederikeHanssen
Merge branch 'dev' into refactor_hc
54c26c7
@asp8200
Trying to input-channels for BCFTOOLS_STATS right
95e9cbb
@asp8200
Fix input-channels for SENTIEON_DEDUP
f288686
@asp8200
Trying to fix input-channels for SNPEFF_SNPEFF
409adb8
@asp8200
Trying to handle Missing process or function map related to VCF_ANNOT…
64ca3f3 
…ATE_SNPEFF
@berguner
fixed tumor_only
1330e1c
@asp8200
Trying to get call to SNPEFF to work
7cdea7c
@asp8200
Still trying to get call to SNPEFF working
78fd7ae
@berguner
clean somatic mutect2
cca3144
@berguner
Merge branch 'dev' of github.com:nf-core/sarek into fix_join_mismatch
7d53f68
@asp8200
Fixing definition of snpeff_cache when downloading snpeff-cache
26c4da9
@FriederikeHanssen @maxulysse
Update workflows/sarek.nf
1f5e174 
Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>
@FriederikeHanssen
Merge branch 'dev' into germline_resource
aaa1f63
@berguner
remove by:0
372f2ee
@FriederikeHanssen
add ugly channel magic beast
1fceca9
maxulysse and others added 29 commits September 12, 2023 16:14
@maxulysse
Merge branch 'dev' into cache_docs_improvements
88f795a
@maxulysse
update CHANGELOG
213c878
@maxulysse @FriederikeHanssen
Apply suggestions from code review
33de708 
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@maxulysse
polish
adc4352
@adamrtalbot
merge stuff
f9938f4
@maxulysse
update
851c5a6
@maxulysse
Merge branch 'cache_docs_improvements' of github.com:adamrtalbot/sare…
c8536d8 
…k into cache_docs_improvements
@maxulysse
polish
45fcca4
@maxulysse
update
c30557c
@maxulysse @adamrtalbot
Apply suggestions from code review
737334c 
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
@maxulysse @adamrtalbot
Update docs/usage.md
a236eab 
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
@adamrtalbot
Merge pull request #1222 from adamrtalbot/cache_docs_improvements
767e4af 
Update documentation around VEP and snpEff cache
@maxulysse
update CHANGELOG
fa0633d
@maxulysse
fix lint warning
545a2ac
@maxulysse
update modules
d4c9d19
@maxulysse
fix lint warning
7bebb39
@maxulysse
Merge pull request #1227 from maxulysse/container_customdump_software
0a3abcc 
FIX: update modules
@FriederikeHanssen
use single sample for spark
a0f5922
@FriederikeHanssen
Merge branch 'dev' into fix_lane
c2a11fe
@FriederikeHanssen
Merge remote-tracking branch 'origin/fix_lane' into fix_lane
65ae3d4
@FriederikeHanssen
Merge pull request #1221 from FriederikeHanssen/fix_lane
29a5c88 
remove lane after tracking in id to ensure proper merging after mapping
@FriederikeHanssen @asp8200
Update nextflow.config
b261eb7 
Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
@FriederikeHanssen @LilyAnderssonLee @asp8200
Apply suggestions from code review
be146c9 
Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
@maxulysse
update CHANGELOG
b3c161a
@maxulysse
update md5sums
5653213
@FriederikeHanssen
Merge pull request #1229 from maxulysse/gatk4_spark_md5sum
587024a 
FIX: gatk4_spark checksum
@FriederikeHanssen
update checksums due to input csv changes
c59e76d
@FriederikeHanssen
update changelog
852d151
@asp8200
Merge pull request #1230 from nf-core/sentieon_checksums
8f6217b 
update checksums due to input csv changes
@asp8200 asp8200 merged commit 1a263a2 into master Sep 13, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@DonFreed DonFreed DonFreed left review comments

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@adamrtalbot adamrtalbot adamrtalbot left review comments

@asp8200 asp8200 asp8200 left review comments

@LilyAnderssonLee LilyAnderssonLee LilyAnderssonLee approved these changes

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

Successfully merging this pull request may close these issues.