- name: Run samtools flagstat test workflow
  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools_flagstat
  files:
    - path: output/samtools/test.paired_end.sorted.bam.flagstat
      md5sum: 80590621c74f5ee43ada20d010a3837f

- name: Run samtools idxstats test workflow
  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_idxstats -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools_idxstats
  files:
    - path: output/samtools/test.paired_end.sorted.bam.idxstats
      md5sum: 3bee8b7d55e412da2b3816c5a18d60d5

- name: Run samtools index test workflow
  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_index -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools_index
  files:
    - path: output/samtools/test.paired_end.sorted.bam.bai
      md5sum: 67338c2995eae82c849830ca55aa7bd1

- name: Run samtools sort test workflow
  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_sort -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools_sort
  files:
    - path: output/samtools/test.bam
      md5sum: a41bfadacd2eeef1d31e05c135cc4f4e

- name: Run samtools stats test workflow
  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_stats -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools_stats
  files:
    - path: output/samtools/test.paired_end.sorted.bam.stats
      md5sum: 06c183864d6e47ab89b0650cae831a93

- name: Run samtools view test workflow
  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_view -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools_view
  files:
    - path: output/samtools/test.bam
      md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff

- name: Run samtools mpileup test workflow
  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_mpileup -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools_mpileup
  files:
    - path: output/samtools/test.mpileup
      md5sum: 95c2646fa7bd535207722008c581c81d