nf-core_modules/tests/software/gatk4/mergevcfs/test.yml

- name: gatk4 mergevcfs test_gatk4_mergevcfs
  command: nextflow run tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c tests/config/nextflow.config
  tags:
    - gatk4_mergevcfs
    - gatk4
  files:
    - path: output/gatk4/test.merged.vcf.gz
      md5sum: ff48f175e26db2d4b2957762f6d1c715

- name: gatk4 mergevcfs test_gatk4_mergevcfs_refdict
  command: nextflow run tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
  tags:
    - gatk4_mergevcfs
    - gatk4
    - gatk4_mergevcfs_refdict
  files:
    - path: output/gatk4/test.merged.vcf.gz
      md5sum: ff48f175e26db2d4b2957762f6d1c715
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 mergevcfs test_gatk4_mergevcfs`
			`command: nextflow run tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c tests/config/nextflow.config`
initial commit adding mergevcfs 2021-02-19 12:29:08 +00:00			`tags:`
			`- gatk4_mergevcfs`
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			`- gatk4`
initial commit adding mergevcfs 2021-02-19 12:29:08 +00:00			`files:`
working test 2021-02-19 12:36:42 +00:00			`- path: output/gatk4/test.merged.vcf.gz`
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 2021-03-09 09:04:08 +00:00			`md5sum: ff48f175e26db2d4b2957762f6d1c715`
added optional reference dictionary as input 2021-02-19 13:09:32 +00:00
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 mergevcfs test_gatk4_mergevcfs_refdict`
			`command: nextflow run tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config`
added optional reference dictionary as input 2021-02-19 13:09:32 +00:00			`tags:`
			`- gatk4_mergevcfs`
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			`- gatk4`
			`- gatk4_mergevcfs_refdict`
added optional reference dictionary as input 2021-02-19 13:09:32 +00:00			`files:`
			`- path: output/gatk4/test.merged.vcf.gz`
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 2021-03-09 09:04:08 +00:00			`md5sum: ff48f175e26db2d4b2957762f6d1c715`