2 commits

Author	SHA1	Message	Date
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
Kevin Menden	a90332906b	add mergebamalignment (#259) ... * add mergebamalignment * fix test.yml * update to latest gatk4 version * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/data/README.md Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/meta.yml * fixed unmapped/unaligned Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-03-17 15:56:56 +01:00