* new mitochondria mode added, tests updated to allow for temp fix for test data
* add cram test
* bam/bam_idx renamed to input and input_index
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
* files created for createsompon, script written, meta written, still needs tests
* updated to 2.0.0 method input, however this requires a genomicsDB input now
* script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests
* versions updated, issue with test data not able to download directory
* updated tests to include repo-side data
* Apply suggestions from code review
* Update modules/gatk4/createsomaticpanelofnormals/main.nf
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* files for learnreadorientationmodel initialised for first commit
* finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted
* updated test data location
* versions file updated, test data added
* updated versions file, edited test file
* small formatting update to main.nf
* Update main.nf
* Update test_data.config
* updated tests main.nf
* Update test_data.config
* Apply suggestions from code review
* Update modules/gatk4/learnreadorientationmodel/main.nf
* Update modules/gatk4/learnreadorientationmodel/meta.yml
* fixed tests failing
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* initiated files for calculate contamination
* pushing local repo to remote
* created script, filled in meta yml, created tests and test yml. local checks passing, needs repo side test data
* added option and tests for outputting optional segmentation file
* saving for test push
* versions updated, test data added
* Update main.nf
* fixed versions info, should report correctly now
* small update to main.nf outputs formatting
* Apply suggestions from code review
* Update test_data.config
* Apply suggestions from code review
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* added output channel for stats file, updated meta yml with description and test yml with check for stats file
* Update modules/gatk4/mutect2/main.nf
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* mutect2 files added, first draft of module code entered
* removing comment from main.nf
* removing comment from main.nf
* test added, commit made before editing yaml
* tests added, still needs final check and info/comments added
* gatk4 version changed to gatk4=4.2.0.0
* multiple sample support added, information added to module yaml file
* Update meta.yml
fixed linting error
* add keywords to meta.yml
* Corrections made to meta.yml
* removed whitespace from meta.yml
Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
* first commit, added template files for new module
* created getpileupsummaries script, tests and both yml files
* fixed typo in meta.yml
* Update modules/gatk4/getpileupsummaries/meta.yml
changed gz_tbi to gz.tbi as suggested
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update README
* Rename pytest_software.yml to pytest_modules.yml
* Rename main software directory to modules
* Remove deprecated modules
* Rename tests software to modules
* Replace paths for tests in pytest_modules.yml
* Replace software with modules in Github Actions
* Replace software with modules in main.nf tests
* Rename software to modules in test.yml
