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
Harshil Patel
5e18e36895
Update and check tests are running for all modules ( #420 )
...
* Fixes for PR 371
* Fix tags
* Add md5sum
* Add md5sums for stringtie
* Fix tests for modules where subtool = build
* Fix pytest_software name conflicts
* Change _ to / in test.yml tags
* Nope...that didnt work
* Fix sequenzautils/bam2seqz tests
2021-04-09 13:47:05 +01:00
suzannejin
989fb7d5b7
modify test path - module gatk4 + added new module gatk4/haplotypecaller ( #382 )
...
* new module: samtools/fastq
* solve conflict: pytest_software.yml
* solve linting conflicts
* solved EditorConfig linting problem
* Module samtools/fastq:
* output compressed fastq.gz file(s)
* add if conditionals for single/paired reads
* samtools/fastq: modified test.yml
* samtools/fastq: modified main.nf to avoid duplicated part of the script section
* fix README.md
* modify test path gatk4
* fix config
* Add new module gatk4/haplotypecaller
* solve check issues
* fix test.yml file
* fix test.yml gz.tbi
* Update software/gatk4/haplotypecaller/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/haplotypecaller/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/haplotypecaller/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/haplotypecaller/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/haplotypecaller/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/gatk4/haplotypecaller/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Apply suggestions from code review
Co-authored-by: suzannejin <suzanne.jin@crg.eu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 12:46:46 +01:00
Maxime Garcia
05cbbbaded
Rename gatk/createsequencedictionary -> gatk4/createsequencedictionary ( #260 )
...
* fix: update and sort filters
* fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary
2021-03-08 14:45:46 +01:00
