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Change --sample by --input #23

Merged
merged 36 commits into from
Sep 10, 2019
Merged

Change --sample by --input #23

merged 36 commits into from
Sep 10, 2019

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maxulysse
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@maxulysse maxulysse commented Aug 14, 2019 •
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I went with:

  • --sample -> --input

For the reference genomes:

  • genomeFile -> fasta
  • genomeDict -> dict
  • genomeIndex -> fastaFai

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 necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Learn more about contributing: https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md

@maxulysse maxulysse requested a review from a team August 14, 2019 08:48
@maxulysse maxulysse added enhancement New feature or request question Further information is requested labels Aug 16, 2019
@maxulysse maxulysse self-assigned this Aug 16, 2019
@maxulysse
feat: update docs
49bc9f0
@maxulysse
Merge branch 'dev' into nf-core-input
420d732
@maxulysse
rename genomeFile, genomeIndex and genomeDict in main.nf script
b418ab9
@maxulysse
Merge remote-tracking branch 'upstream/dev' into nf-core-input
6c64cd4
@maxulysse
add deprecation message
0611d09
@maxulysse
better deprecation message
fab5387
@maxulysse
update docs
1afdf58
@maxulysse
update docs
37719d2
@maxulysse
Merge branch 'nf-core-input' of github.com:MaxUlysse/Sarek into nf-co…
5726f3a 
…re-input
@maxulysse
Refactor deprecation for --sample, --sampleDir, --anotateVCF, --noRep…
6714f8e 
…orts, --genomeDict, --genomeFile, --genomeIndex

- Add message when deprecated params are used
- Deprecated params are still working

- Fix usage of deprecated params

-
@maxulysse
move modifications to another branch
acb59b4
@maxulysse
Fix --input for germline sample directory
7f5637b 
- tsvPath is now defined as null by default
@maxulysse
Add GitHubActions (nf-core#27)
cc6750d 
* feat: Add GitHubActions
* feat: reduce linting time
* feat: add --memory for script
* feat: use --max_memory to limit memory usage to 6.GB on GitHub actions
* install nextflow directly
* try matrix
* use export to get correct nextflow version
* add linting tests
* fix with node version indent
* rename jobs
* code polish
* feat: add badges for GitHub Actions
* test branch protection
@maxulysse
fix syntax hopefully
22dff1b
@maxulysse
Merge remote-tracking branch 'upstream/dev' into nf-core-input
61befb3
@maxulysse maxulysse requested review from szilvajuhos and a team September 9, 2019 09:29
szilvajuhos
szilvajuhos approved these changes Sep 9, 2019
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Thanks, looks OK

@maxulysse maxulysse merged commit 5ea919f into nf-core:dev Sep 10, 2019
@maxulysse maxulysse deleted the nf-core-input branch September 10, 2019 18:51
@Poocee Poocee mentioned this pull request Jul 29, 2024
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@szilvajuhos szilvajuhos szilvajuhos approved these changes

@apeltzer apeltzer apeltzer approved these changes

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@maxulysse @apeltzer @szilvajuhos