suzannejin
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989fb7d5b7
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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>
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2021-03-26 12:46:46 +01:00 |
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Harshil Patel
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acb1a12a56
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Re-organise all test data (#354)
* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
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2021-03-24 09:53:41 +00:00 |
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Kevin Menden
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a552d97849
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Exchange VCF data by sarscov2 data (#261)
* added sarscov2 vcf data; adjusted bcftools tests
* updated README.md
* deleted old VCF files; fixed mergevcfs
* fixed tabix
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2021-03-09 10:04:08 +01:00 |
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kevinmenden
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02abe106ec
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added optional reference dictionary as input
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2021-02-19 14:09:32 +01:00 |
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kevinmenden
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3ac5c5fad6
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working test
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2021-02-19 13:36:42 +01:00 |
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kevinmenden
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c288e081b4
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initial commit adding mergevcfs
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2021-02-19 13:29:08 +01:00 |
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