* Added: gatk4/leftalignandtrimvariants
Additions:
- GATK4/LeftAlignAndTrimVariants module
- Use sars-ncov2 test data as this normalises a larger INDEL correctly.
Fixes#1801
* fixup: Added index to output spec
* fixup: Pattern of tbi output corrected to 'tbi'
* gatk4/leftalignandtrimvariants: Added intervals
Changes:
- gatk4/leftalignandtrimvariants now supports optional interval as BED
file
- Tests added with and without interval. Not test BED file excludes all
variants so no variants are actually normalised.
Fixes#1801
* fixup: leftalignandtrimvariants vcf->tbi fix
* fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
vcf2maf module created
Additions:
- vcf2maf module created
- If VEP is present in PATH, it is added to command
- If VEP is missing, it is ignored (recommended to skip with --inhibit-vep)
- VEP version automatically added to versions.yml
- Uses VEP cache during testing which is added to test-datasets in https://github.com/nf-core/test-datasets/pull/563
- Default Docker image includes VEP and vcf2maf
- Test includes without VEP.
Relates to #490
* Trimmomatic main only first draft
* Add test files
* SE PE Adjustment
* Remove extra reads input
* chore: Remove TODOs
* Apply suggestions from code review
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* fix(trimmomatic): Handle SE output correctly
Since there's never going to be unpaired reads for SE reads we can get
away with it for SE
* fix(trimmomatic): Use correct elvis operator to handle logic
* fix(trimmomatic): Add hack to work with SE and PE reads
* Update test.yml
* use the PE and SE trimming correctly
* Made user set adaptors
* Add documentation
* test(trimmomatic): Add files to pytest_modules
* test(trimmomatic): Update name of failing test
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* update bclconvert module, as used in nf-core/demultiplex
* reconfigure test with new test data
* update test
* formatting
* update outputs, update meta
* update module and test
* update test config, test.yml
* fix linting
* emit logs and reports as dir
* fix typo, recreate test.yml
* fix linting
Co-authored-by: CMGG ICT Team <ict@cmgg.be>
* Making the output from the VEP-moduel (ENSEMBLVEP) optionally vcf, json or tab. #1774
* Trying to fix tests
* Still trying to fix tests
* Fetching the vep-output-file-extension from the args.
* Update meta.yml
* WIP: Adding tests for vep-output json and tab
* updated the test.yml
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: nvnieuwk <nicolas.vannieuwkerke@ugent.be>
* Add module definition for kreport2krona
* Add metadata for kreport2krona module
* Add tests for kreport2krona
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Add atlas/splitmerge module
* Finish the tests for atlas/splitmerge
* Prettier
* Update modules/atlas/splitmerge/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Remove curly brackets from meta.yml parameters
For single-file outputs, as reviewed
* Lintung: Remove trailing white-space
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
