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Actual 3.0 release - this is the real one #672

Merged
merged 2,793 commits into from
Jul 21, 2022
Merged

Actual 3.0 release - this is the real one #672

merged 2,793 commits into from
Jul 21, 2022

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maxulysse
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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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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).
  • 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).

FriederikeHanssen and others added 30 commits July 18, 2022 15:54
@FriederikeHanssen
change results folder structure
b57db9a
@maxulysse
forgot conflicts
93b241b
@FriederikeHanssen
merge upstream/dev
e42b281
@FriederikeHanssen
update changelog & docs
3b576c1
@maxulysse
why 2 bams in single_bam?
e9a3362
fix no_intervals and tests
0ea9747
@maxulysse
update CHANGELOG
68f61ae
lint
0717286
update to dev
37e5e77
@maxulysse
channel magic for skip or not markduplicates
eec5eb0
lint
1db8bc8
fix empty module
ff6b530
@asp8200
Allow any step but annotation to start from bam-files
2b034da
@ggabernet
Merge pull request #652 from ggabernet/dev
9afe650 
add full size tests somatic
@maxulysse
fix tests
20db917
correct prepare_genome input
aa7127a
@FriederikeHanssen
Merge remote-tracking branch 'upstream/dev' into file_structure
ef7f9cb
@FriederikeHanssen
update paths in test files
570a357
@maxulysse
improve csv creation when skipping markduplicates + update tests
e4a2ab1
@maxulysse
fix paths
82e32d1
@maxulysse
fix logic
934a0dd
@FriederikeHanssen
Merge pull request #653 from FriederikeHanssen/file_structure
0bf6676 
File structure for results should be coherent between reports and preprocessing
@asp8200
Merge branch 'dev' into adjust_checks_step_plus_csv
93be3b0
@asp8200
Updating changelog
783b4d2
@asp8200
Removing redundant blank line
9be3c5c
@FriederikeHanssen
own subworkflow for cnvkit references
91bbf3d
@FriederikeHanssen
add comment back in
46cc19c
@apeltzer
Merge pull request #654 from asp8200/adjust_checks_step_plus_csv
3a0d841 
DRAFT: Allow any step but annotation to start from bam-files
@FriederikeHanssen
why does this work
fd48c58
@FriederikeHanssen
this works aside from versions parsing
2e65182
FriederikeHanssen and others added 22 commits July 20, 2022 18:48
@FriederikeHanssen
Merge pull request #660 from FriederikeHanssen/release_review
6f41b7c 
Review Comments for release
@FriederikeHanssen
Merge remote-tracking branch 'upstream/dev' into docs_igenomes
395651d
@FriederikeHanssen
remove duplicated sections
0bc9403
@FriederikeHanssen
Merge pull request #673 from FriederikeHanssen/docs_igenomes
d6bb67b 
Update igenomes sections and final polish of docs
@nickhsmith
Merge branch 'dev' into vqsr
d842fe0
@FriederikeHanssen
tiny memory update + split fastq default value as discussed on slack
80e08d8
@FriederikeHanssen
change log
06e3f46
@FriederikeHanssen
forgot to cite eager for subway map
8eaf5e7
@FriederikeHanssen
we don't have 50000000 test reads, so 0 for testing
6bd0051
@nickhsmith
fix haplotypecaller cram input
73e84db
@FriederikeHanssen
only remove sharded number for duplicate marking, and only at the ver…
b63e4ee 
…y end
@FriederikeHanssen
Merge pull request #675 from FriederikeHanssen/cite
00aa3d5 
forgot to cite eager for subway map
@FriederikeHanssen
fix indents, commas etc
9fa1a5c
@FriederikeHanssen
no default, and ploidy is a number
6c7f310
@nickhsmith
remove test file
b0c32c7
@maxulysse
update version
51c6d6a
@FriederikeHanssen
Merge pull request #595 from nickhsmith/vqsr
21b9f62 
Joint Germline subworkflow haplotypecaller -> Vqsr
@FriederikeHanssen
Merge pull request #674 from FriederikeHanssen/small_ressource
25d91c2 
tiny memory update + split fastq default value as discussed on slack
@FriederikeHanssen
merge upstream/dev
c54e097
@FriederikeHanssen
Merge remote-tracking branch 'upstream/dev' into update_igenomes
19846b0
@FriederikeHanssen
merge upstream/dev
1351292
@apeltzer
Merge pull request #676 from maxulysse/dev_3.0
c6cbec7 
update version
@apeltzer apeltzer added this to the 3.0 milestone Jul 21, 2022
@FriederikeHanssen FriederikeHanssen merged commit 5bb160d into master Jul 21, 2022
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@ggabernet ggabernet ggabernet approved these changes

@apeltzer apeltzer apeltzer approved these changes

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8 participants
@maxulysse @apeltzer @ggabernet @FriederikeHanssen @asp8200 @WackerO @nickhsmith @SusiJo