James A. Fellows Yates
3cc43838e1
module: picard filtersamreads ( #602 )
...
* Start work filtersamreads
* Refactored to allow optional input
* Use proper readlist test data
* Remove typo
* Fix if else condition
* Remove debugging code
* Fix container URLs
* Add required input specification meta
* Cleanup
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fix suffixing
* Additional formatting tweaks
* Update modules/picard/filtersamreads/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update modules/picard/filtersamreads/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 15:22:19 +01:00
James A. Fellows Yates
1a26d48104
module: picard sortsam ( #603 )
...
* Add picard/sortsam module
* Fix container links
* Changes after code review
* Input meta in the right place
2021-07-21 13:48:07 +02:00
Harshil Patel
e4df336294
Add hifiasm module ( #596 )
...
* Add hifiasm module
* Tidy up module
* Add pacbio files to test_data.config
2021-07-20 21:50:22 +01:00
Johnathan D
2e619add87
Add samtools ampliconclip ( #590 )
...
* created template for `samtools/ampliconclip` (#584 )
* All tests passing (#584 )
* Linting fixed (#584 )
* Final linting fixed (#584 )
* Optional output flags moved to `input` (#584 )
* typo fix (#584 )
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-20 21:31:31 +01:00
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure ( #567 )
...
* 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
2021-07-07 10:10:18 +01:00
