* Add ultra/index and ultra/align modules
* Correct tag and prefix
* Fix typos
* Remove SAMTOOLS SORT from test
* Update: Convert sam to bam
* Add tag to docker image
* Fix typo
* Add args2 for samtools
* Support non-GFF input
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Fix linting error
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* changing mv by gzip
* changing mv by gzip
* first module creation
* add test.yml
* add flye to pyestes_modules.yml
* update flye module
* delete functions.nf
* generate test.yml
* fix contains from test.yml
* test file assembly_info.txt with regex
* check that file contains at least contig_1
* fix typo in contains
* update version
* split fastq file for raw runs
* use asm-coverage to reduce memory usage
* fix module name error
* add genome-size
* decrease coverage
* change test data for raw runs
* add coverage and genome size
* Apply comments from code review
Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
* after many trys, add a stub run
* remove md5sum for stub run
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix review comments
* Apply suggestions from code review
Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
* no hardcoded version in stub run
* Update modules/flye/main.nf
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
NGSCheckMate doesn't generate a pdf if only one sample is included, made optional
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Add rgi database version to module as fixed within the container/environment
* Remove check of the version file
* Or rather check for existance of the versions file not contents
* Delete main.nf
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* 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>
