- name: ismapper-test
  command: bash -c 'nextflow run ./subworkflows/local/ismapper/test.nf -entry test_ismapper --wf ismapper -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - ismapper
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/ismapper/nf-reports/ismapper-dag.dot
      contains: ['ismapperdag', 'ISMAPPER', 'versions']
    - path: bactopia/bactopia-runs/ismapper/nf-reports/ismapper-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/ismapper/nf-reports/ismapper-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/ismapper/nf-reports/ismapper-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702_IS1016V1_IS1595_IS1016_left_final.fastq
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702_IS1016V1_IS1595_IS1016_right_final.fastq
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702__NC_018507.1_closest.bed
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702__NC_018507.1_intersect.bed
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702__NC_018507.1_table.txt
      md5sum: 9e05cda3990cb841db2bfb6e6e04a1f5
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702_left_NC_018507.1_finalcov.bed
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702_left_NC_018507.1_merged.sorted.bed
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702_left_NC_018507.1_unpaired.bed
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702_right_NC_018507.1_finalcov.bed
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702_right_NC_018507.1_merged.sorted.bed
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/IS1016V1_IS1595_IS1016/SRR2838702_right_NC_018507.1_unpaired.bed
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/logs/SRR2838702.log
      contains: ['samtools', 'bedtools', 'finished']
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/logs/nf-ismapper.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/logs/nf-ismapper.err
      contains: ['bwa_index', 'Version', 'Real']
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/logs/nf-ismapper.log
      contains: ['bwa_index', 'Version', 'Real']
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/logs/nf-ismapper.out
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/logs/nf-ismapper.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/logs/nf-ismapper.sh
      contains: ['ismap', 'END_VERSIONS']
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/logs/nf-ismapper.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR2838702/tools/ismapper/ismapper/logs/versions.yml
      md5sum: eda0743d59eda7b33011608a6f5316f6
