nf-core_modules/tests/modules/gatk4/splitncigarreads/test.yml

- name: gatk4 splitncigarreads test_gatk4_splitncigarreads
  command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
  tags:
    - gatk4
    - gatk4/splitncigarreads
  files:
    - path: output/gatk4/test.bam
      md5sum: 8d05a41f9467e62d3fc1bc725f0869ec
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 07:46:46 -04:00			`- name: gatk4 splitncigarreads test_gatk4_splitncigarreads`
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 05:10:18 -04:00			`command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config`
adding SplitNCigarReads 2021-02-19 08:59:29 -05:00			`tags:`
			`- gatk4`
Lint modules ci (#389) * 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 04:10:52 -04:00			`- gatk4/splitncigarreads`
adding SplitNCigarReads 2021-02-19 08:59:29 -05:00			`files:`
Modules TLC (#551) * Modules TLC * Fix all the tests 2021-07-01 11:13:01 -04:00			`- path: output/gatk4/test.bam`
fix: update to gatk4.2.0.0 (#575) * fix: update to gatk4.2.0.0 * fix: update md5sum 2021-07-16 05:26:28 -04:00			`md5sum: 8d05a41f9467e62d3fc1bc725f0869ec`