Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure ( #567 )
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* 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
suzannejin
989fb7d5b7
modify test path - module gatk4 + added new module gatk4/haplotypecaller ( #382 )
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* 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
Harshil Patel
acb1a12a56
Re-organise all test data ( #354 )
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* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
2021-03-24 09:53:41 +00:00
Kevin Menden
a552d97849
Exchange VCF data by sarscov2 data ( #261 )
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* added sarscov2 vcf data; adjusted bcftools tests
* updated README.md
* deleted old VCF files; fixed mergevcfs
* fixed tabix
2021-03-09 10:04:08 +01:00
kevinmenden
02abe106ec
added optional reference dictionary as input
2021-02-19 14:09:32 +01:00
kevinmenden
3ac5c5fad6
working test
2021-02-19 13:36:42 +01:00
kevinmenden
c288e081b4
initial commit adding mergevcfs
2021-02-19 13:29:08 +01:00
