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merge dsl2 into dev #417

Merged
merged 559 commits into from
Aug 3, 2021
Merged

merge dsl2 into dev #417

merged 559 commits into from
Aug 3, 2021

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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).

maxulysse and others added 30 commits March 23, 2021 11:43
@maxulysse
fix: simplify markduplicates subworkflow
159fe57
@maxulysse
fix: --input tests with folder
86e76e5
@maxulysse
fix: extension for samtools_merge module
6d48b9f
@maxulysse
fix: fix haplotypecaller
e1abc27
@maxulysse
feat: update bwa/bwamem2 containers
64ea14f
@maxulysse
Merge pull request nf-core#358 from MaxUlysse/dsl2_modules
6b57759 
Update dsl2 modules
@maxulysse
fix: correct hash for mulled containers to fix nf-core#364
11bcd92
@maxulysse
Merge pull request nf-core#366 from MaxUlysse/dsl2_bwa_bwamem2
656bb85 
Correct hash in mulled bwa/bwa-mem2 | samtools containers
@maxulysse
feat: remove social preview image to use GitHub OpenGraph
85d6c0d
@ewels
Merge pull request nf-core#369 from maxulysse/dsl2
cfe37e4 
Remove social preview image to use GitHub OpenGraph
@maxulysse
feat: add pytest workflow for default and aligner
fa5576c
@edmundmiller
ci: Add local modules pytest-workflow workflow
db6a6cf
@edmundmiller
test: Add infrastructure
96b012b
@edmundmiller
test(markduplicates): Add initial test
f517e06
@edmundmiller
test: Add modules config for default settings
6c8397e
@maxulysse
Merge pull request #6 from Emiller88/dsl2-subworkflow-tests
737cedf 
Dsl2 subworkflow tests
@maxulysse @edmundmiller
Apply suggestions from code review
00fc1e7 
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
@maxulysse
feat: immprove tests
645bdc5
@maxulysse
fix: comments
b22e28a
@maxulysse
feat: add gatk4 tests
39d19f8
@maxulysse
fix: no need for gatk4 tests here
b3b82a4
@maxulysse
feat: more tests, and more complete
a2a0818
@maxulysse
feat: add tests for variant calling
4c5e0a8
@maxulysse
feat: more tests incoming with pytest
765d017
@maxulysse
feat: clean up tests
c016b59
@maxulysse
Merge pull request nf-core#370 from maxulysse/dsl2_tests
13f61c1 
Add pytest workflow for CI
@maxulysse
Merge remote-tracking branch 'upstream/dev' into dsl2
465ceae
@maxulysse
fix: Nextflow version
7d90b4d
@maxulysse
Merge remote-tracking branch 'upstream/dev' into dsl2
d8a5722
@maxulysse @FriederikeHanssen
Apply suggestions from code review
617f407 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
maxulysse and others added 22 commits July 16, 2021 15:18
@maxulysse
fix: nf-core lint
84af6f8
@maxulysse
fix: workflow is back
94951d6
@maxulysse
fix: bwa/mem and bwamem2/mem modules
2f69572
@maxulysse
fix: update modules
7844ee8
@maxulysse
fix: genome loading in profiles
472e721
@maxulysse
fix: multiqc args
b0d2798
@maxulysse
fix: bam -> cram
2ad6bcd
@maxulysse
fix: merge output names
675bca9
@maxulysse
Merge pull request nf-core#408 from maxulysse/nf-core-template-merge-…
fa99d8e 
…2.0.1

Nf core template merge 2.0.1
@maxulysse
fix: update CI tests
c41a127
@maxulysse
fix: remove variant_calling test
6a270cb
@maxulysse
fix: annotate
9c35d4d
@maxulysse
fix: multiqc output for CI
dd7bb00
@maxulysse
fix: remove only msi tests
fb97387
@maxulysse
Merge pull request nf-core#410 from maxulysse/dsl2_CI
05194ed 
fix: update CI tests
@maxulysse
fix: ban -> cram in CSV
09c4b75
@maxulysse
fix: CSV back in CI tests
c301e74
@maxulysse
Merge pull request nf-core#411 from maxulysse/dsl2_updates
2fae194 
bam -> cram in CSV
@nf-core-bot
Template update for nf-core/tools version 2.1
8244911
@maxulysse
Merge branch 'dsl2' into nf-core-template-merge-2.1
5f5330c
@maxulysse
Merge pull request nf-core#416 from nf-core/nf-core-template-merge-2.1
8f95fd8 
Important! Template update for nf-core/tools v2.1
@maxulysse
Merge remote-tracking branch 'upstream/dsl2' into dev
c17aeb5
@maxulysse
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Once approved and merged, we can change the base branch for #412 and delete the dsl2 branch.

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github-actions bot commented Jul 28, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f8ba00d

+| ✅ 135 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in main.nf: List additional required output channels/values here
  • pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
  • pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-07-28 20:00:31

@maxulysse maxulysse mentioned this pull request Aug 3, 2021
Merged
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FriederikeHanssen
FriederikeHanssen approved these changes Aug 3, 2021
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Looks good to me. Massive PR, but most has been reviewed before in the dsl2 branch.

conf/genomes.config Show resolved Hide resolved
@maxulysse maxulysse merged commit 4d5f3dc into nf-core:dev Aug 3, 2021
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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7 participants
@maxulysse @FriederikeHanssen @ewels @edmundmiller @abhi18av @KevinMenden @nf-core-bot