Kevin Menden
043a7d1e3c
remove deprecated test tags ( #440 )
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* remove deprecated test tags
* fix bowtie, gatk4/applybsqr
* fix gatk4 baserecalibrator
* fixed shovill
* fixed yara/mapper
* fixed kallistobustools/ref paths
2021-04-13 18:03:09 +01:00
Edmund Miller
a3684d9594
Lint modules ci ( #389 )
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* ci: Add modules lint step
Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup
* ci: _ => /
* Update tests/config/pytest_software.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 09:10:52 +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
yocra3
614d61dc13
Add gatk4/applybqsr ( #331 )
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* Add applybqsr module
* Solve problem in functions.nf
* Add to pytest
2021-03-23 14:15:26 +01:00
