- name: bowtie2 align test_bowtie2_align_single_end
  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
  tags:
    - bowtie2
    - bowtie2/align
  files:
    - path: ./output/bowtie2/test.bam
    - path: ./output/bowtie2/test.bowtie2.log
    - path: ./output/bowtie2/versions.yml

- name: bowtie2 align test_bowtie2_align_single_end_sorted
  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_sorted -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
  tags:
    - bowtie2
    - bowtie2/align
  files:
    - path: ./output/bowtie2/test.bam
    - path: ./output/bowtie2/test.bowtie2.log
    - path: ./output/bowtie2/versions.yml

- name: bowtie2 align test_bowtie2_align_paired_end
  command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config
  tags:
    - bowtie2
    - bowtie2/align
  files:
    - path: ./output/bowtie2/test.bam
    - path: ./output/bowtie2/test.bowtie2.log
    - path: ./output/bowtie2/versions.yml

- name: bowtie2 align test_bowtie2_align_single_end_large_index
  command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index
  tags:
    - bowtie2
    - bowtie2/align
  files:
    - path: ./output/bowtie2/test.bam
    - path: ./output/bowtie2/test.bowtie2.log
    - path: ./output/bowtie2/versions.yml

- name: bowtie2 align test_bowtie2_align_paired_end_large_index
  command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index
  tags:
    - bowtie2
    - bowtie2/align
  files:
    - path: ./output/bowtie2/test.bam
    - path: ./output/bowtie2/test.bowtie2.log
    - path: ./output/bowtie2/versions.yml