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Prepare 3.0 release #631

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wants to merge 2,632 commits into from
Closed

Prepare 3.0 release #631

wants to merge 2,632 commits into from

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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).

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @maxulysse,

It looks like this pull-request is has been made against the maxulysse/nf-core_sarek master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the maxulysse/nf-core_sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@maxulysse maxulysse marked this pull request as draft July 13, 2022 10:56
@maxulysse maxulysse marked this pull request as ready for review July 14, 2022 09:18
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github-actions bot commented Jul 17, 2022 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b9a891c

+| ✅ 146 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_description - No description provided in schema for parameter: ascat_ploidy

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-20 14:16:29

maxulysse and others added 26 commits July 17, 2022 16:17
@maxulysse
update skip_markduplicates tests
0150003
@maxulysse
fix mosdepth
f1453a3
@FriederikeHanssen
update umi checksums
e053000
@FriederikeHanssen
no need to overwrite the dragmap prefix, it is the same
0e40b6a
@FriederikeHanssen
remove checksum for collated bam file
eb07bf0
@FriederikeHanssen
if reference is provided then no bed file
fb1e756
@FriederikeHanssen
have freebayes only use a single core, parallel implementation isn't …
440d2f9 
…adding anything in our etup
@FriederikeHanssen
add warn if intervals is provided without wes
85afefc
@FriederikeHanssen
combine conditionals
62e182e
@FriederikeHanssen
fix pon validation
1411796
@FriederikeHanssen
Merge pull request nf-core#614 from WackerO/umi
e8d484f 
Umi test
@maxulysse
Merge pull request nf-core#646 from FriederikeHanssen/params
5dc3f3b 
Nextflow_schema.json updates
@maxulysse
Merge remote-tracking branch 'upstream/dev' into dev_modules_update
442d9b5
@maxulysse
Merge remote-tracking branch 'upstream/dev' into 3.0
8b9183d
@maxulysse
fix output
9194d97
@maxulysse
fix output
3e7bdd8
@maxulysse
Merge pull request nf-core#633 from maxulysse/dev_modules_update
5b83a5d 
nf-core modules update -a
@maxulysse
Merge remote-tracking branch 'upstream/dev' into 3.0
f4055c8
@maxulysse
update aligner tests expected files
770881c
@FriederikeHanssen
Add vague statement about md and bqsr
7600d62
@FriederikeHanssen
Add comments about bwa parameters
3f1002e
@FriederikeHanssen
add comment on empty snpeff plots in multiqc
0064a9c
@maxulysse
Merge pull request nf-core#648 from FriederikeHanssen/param_valid
45aab1c 
PON not correctly validated
@maxulysse
Merge remote-tracking branch 'upstream/dev' into dev_tests_yml
ee4b556
@maxulysse
fix output for targete bed
4ecd84e
@maxulysse
code polish
c39047a
FriederikeHanssen and others added 18 commits July 20, 2022 10:23
@FriederikeHanssen
remove task.ext.args that is not used in local module
7082782
@maxulysse
Merge branch 'dev' into index_svg
2fd6afd
@WackerO
Updated SVDB module
081f8e2
@WackerO
Merge branch 'dev' of https://github.com/nf-core/sarek into svdb
c43ea10
@maxulysse
Merge pull request nf-core#666 from SusiJo/multiqc_channels
d1402dd 
Simplify multiqc config channels
@maxulysse
Merge pull request nf-core#655 from FriederikeHanssen/intervals_fasta
3720676 
Fix --intervals false
@WackerO @maxulysse
Update conf/modules.config
da917e1 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
@maxulysse
Merge pull request nf-core#665 from ggabernet/fulltests
08f130b 
add split fastq to test full
@WackerO @maxulysse
Update conf/modules.config
c48b7f1 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
@FriederikeHanssen
Merge pull request nf-core#661 from FriederikeHanssen/index_svg
93a4925 
add cnvkit index
@maxulysse
Merge remote-tracking branch 'upstream/dev' into 3.0
c064aee
@maxulysse
Merge branch '3.0' into dev_3.0_PR
db7024e
@WackerO
Updated module again
da6cfc9
@WackerO
Merge branch 'dev' of https://github.com/nf-core/sarek into svdb
d47bb26
@WackerO
Merge branch 'svdb' of https://github.com/WackerO/sarek into svdb
ba020b3
@maxulysse
remove duplication
fc50739
@maxulysse
fix path to file in csv files
335396a
@maxulysse
update CHANGELOG
a36e697
lescai
lescai reviewed Jul 20, 2022
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I've improved the documentation for UMI read structure. Thanks for the suggestions, it's not the simplest topic to explain in short.

docs/usage.md Show resolved Hide resolved
maxulysse and others added 6 commits July 20, 2022 14:02
@maxulysse @asp8200
Apply suggestions from code review
fc09504 
Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
@WackerO
Updated test
b1ce5bb
@maxulysse
Merge pull request nf-core#669 from maxulysse/dev_restart_csv
cff880f 
fix path to file in csv files
@maxulysse
Merge remote-tracking branch 'upstream/dev' into 3.0
23453e8
@maxulysse
Merge pull request nf-core#664 from maxulysse/dev_3.0_PR
467b2e6 
Update comments merged on the 3.0 PR back to dev
@maxulysse
Merge pull request nf-core#667 from WackerO/svdb
3441df4 
SVDB MERGE update
@maxulysse
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Replaced by #672

lescai
lescai reviewed Jul 20, 2022
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README.md Show resolved Hide resolved
@maxulysse maxulysse closed this Jul 20, 2022
@maxulysse maxulysse deleted the 3.0 branch September 5, 2022 12:25
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@ggabernet ggabernet ggabernet approved these changes

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9 participants
@maxulysse @apeltzer @ggabernet @FriederikeHanssen @mahesh-panchal @WackerO @SusiJo @lescai @asp8200