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: ceed15c0bd64ff5c38d3816905933b0b
    - path: output/gatk4/versions.yml
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 11:46:46 +00:00			`- name: gatk4 splitncigarreads test_gatk4_splitncigarreads`
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead 2021-12-20 16:10:49 +00:00			`command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config`
adding SplitNCigarReads 2021-02-19 13:59:29 +00:00			`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 08:10:52 +00:00			`- gatk4/splitncigarreads`
adding SplitNCigarReads 2021-02-19 13:59:29 +00:00			`files:`
Modules TLC (#551) * Modules TLC * Fix all the tests 2021-07-01 15:13:01 +00:00			`- path: output/gatk4/test.bam`
Update versions (#1292) * Update versions * update checksums + remove variables as input for applyvqsr * sneak in removal of values and provide them via modules.config * update another checksum * more checksums * move vairable to config * remove controlfreec, wrong branch * add line break 2022-02-15 10:29:36 +00:00			`md5sum: ceed15c0bd64ff5c38d3816905933b0b`
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead 2021-12-20 16:10:49 +00:00			`- path: output/gatk4/versions.yml`