- name: star align test_star_alignment_single_end
  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
  tags:
    - star/align
    - star
  files:
    - path: output/star/star/Genome
      md5sum: a654229fbca6071dcb6b01ce7df704da
    - path: output/star/star/Log.out
    - path: output/star/star/SA
      md5sum: 8c3edc46697b72c9e92440d4cf43506c
    - path: output/star/star/SAindex
      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
    - path: output/star/star/chrLength.txt
      md5sum: c81f40f27e72606d7d07097c1d56a5b5
    - path: output/star/star/chrName.txt
      md5sum: 5ae68a67b70976ee95342a7451cb5af1
    - path: output/star/star/chrNameLength.txt
      md5sum: b190587cae0531f3cf25552d8aa674db
    - path: output/star/star/chrStart.txt
      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
    - path: output/star/star/exonGeTrInfo.tab
      md5sum: d04497f69d6ef889efd4d34fe63edcc4
    - path: output/star/star/exonInfo.tab
      md5sum: 0d560290fab688b7268d88d5494bf9fe
    - path: output/star/star/geneInfo.tab
      md5sum: 8b608537307443ffaee4927d2b428805
    - path: output/star/star/genomeParameters.txt
      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
    - path: output/star/star/sjdbInfo.txt
      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
    - path: output/star/star/sjdbList.fromGTF.out.tab
      md5sum: 8760c33e966dad0b39f440301ebbdee4
    - path: output/star/star/sjdbList.out.tab
      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
    - path: output/star/star/transcriptInfo.tab
      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
    - path: output/star/test.Aligned.out.bam
      md5sum: 63de6af2210e138b49d7b4d570c6e67f
    - path: output/star/test.Log.final.out
    - path: output/star/test.Log.out
    - path: output/star/test.Log.progress.out
    - path: output/star/test.SJ.out.tab

- name: star align test_star_alignment_paired_end
  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
  tags:
    - star/align
    - star
  files:
    - path: output/star/star/Genome
      md5sum: a654229fbca6071dcb6b01ce7df704da
    - path: output/star/star/Log.out
    - path: output/star/star/SA
      md5sum: 8c3edc46697b72c9e92440d4cf43506c
    - path: output/star/star/SAindex
      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
    - path: output/star/star/chrLength.txt
      md5sum: c81f40f27e72606d7d07097c1d56a5b5
    - path: output/star/star/chrName.txt
      md5sum: 5ae68a67b70976ee95342a7451cb5af1
    - path: output/star/star/chrNameLength.txt
      md5sum: b190587cae0531f3cf25552d8aa674db
    - path: output/star/star/chrStart.txt
      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
    - path: output/star/star/exonGeTrInfo.tab
      md5sum: d04497f69d6ef889efd4d34fe63edcc4
    - path: output/star/star/exonInfo.tab
      md5sum: 0d560290fab688b7268d88d5494bf9fe
    - path: output/star/star/geneInfo.tab
      md5sum: 8b608537307443ffaee4927d2b428805
    - path: output/star/star/genomeParameters.txt
      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
    - path: output/star/star/sjdbInfo.txt
      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
    - path: output/star/star/sjdbList.fromGTF.out.tab
      md5sum: 8760c33e966dad0b39f440301ebbdee4
    - path: output/star/star/sjdbList.out.tab
      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
    - path: output/star/star/transcriptInfo.tab
      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
    - path: output/star/test.Aligned.out.bam
      md5sum: 7cdef439bc8092bfefb4d091bf8ee6ab
    - path: output/star/test.Log.final.out
    - path: output/star/test.Log.out
    - path: output/star/test.Log.progress.out
    - path: output/star/test.SJ.out.tab

- name: star align test_star_alignment_paired_end_for_fusion
  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end_for_fusion -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
  tags:
    - star/align
    - star
  files:
    - path: output/star/star/Genome
      md5sum: a654229fbca6071dcb6b01ce7df704da
    - path: output/star/star/Log.out
    - path: output/star/star/SA
      md5sum: 8c3edc46697b72c9e92440d4cf43506c
    - path: output/star/star/SAindex
      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
    - path: output/star/star/chrLength.txt
      md5sum: c81f40f27e72606d7d07097c1d56a5b5
    - path: output/star/star/chrName.txt
      md5sum: 5ae68a67b70976ee95342a7451cb5af1
    - path: output/star/star/chrNameLength.txt
      md5sum: b190587cae0531f3cf25552d8aa674db
    - path: output/star/star/chrStart.txt
      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
    - path: output/star/star/exonGeTrInfo.tab
      md5sum: d04497f69d6ef889efd4d34fe63edcc4
    - path: output/star/star/exonInfo.tab
      md5sum: 0d560290fab688b7268d88d5494bf9fe
    - path: output/star/star/geneInfo.tab
      md5sum: 8b608537307443ffaee4927d2b428805
    - path: output/star/star/genomeParameters.txt
      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
    - path: output/star/star/sjdbInfo.txt
      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
    - path: output/star/star/sjdbList.fromGTF.out.tab
      md5sum: 8760c33e966dad0b39f440301ebbdee4
    - path: output/star/star/sjdbList.out.tab
      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
    - path: output/star/star/transcriptInfo.tab
      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
    - path: output/star/test.Aligned.out.bam
      md5sum: 5dbc36fce7b72628c809bbc7d3d67973
    - path: output/star/test.Log.final.out
    - path: output/star/test.Log.out
    - path: output/star/test.Log.progress.out
    - path: output/star/test.SJ.out.tab

- name: star align test_star_alignment_paired_end_for_starfusion
  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end_for_starfusion -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
  tags:
    - star/align
    - star
  files:
    - path: output/star/star/Genome
      md5sum: a654229fbca6071dcb6b01ce7df704da
    - path: output/star/star/Log.out
    - path: output/star/star/SA
      md5sum: 8c3edc46697b72c9e92440d4cf43506c
    - path: output/star/star/SAindex
      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
    - path: output/star/star/chrLength.txt
      md5sum: c81f40f27e72606d7d07097c1d56a5b5
    - path: output/star/star/chrName.txt
      md5sum: 5ae68a67b70976ee95342a7451cb5af1
    - path: output/star/star/chrNameLength.txt
      md5sum: b190587cae0531f3cf25552d8aa674db
    - path: output/star/star/chrStart.txt
      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
    - path: output/star/star/exonGeTrInfo.tab
      md5sum: d04497f69d6ef889efd4d34fe63edcc4
    - path: output/star/star/exonInfo.tab
      md5sum: 0d560290fab688b7268d88d5494bf9fe
    - path: output/star/star/geneInfo.tab
      md5sum: 8b608537307443ffaee4927d2b428805
    - path: output/star/star/genomeParameters.txt
      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
    - path: output/star/star/sjdbInfo.txt
      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
    - path: output/star/star/sjdbList.fromGTF.out.tab
      md5sum: 8760c33e966dad0b39f440301ebbdee4
    - path: output/star/star/sjdbList.out.tab
      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
    - path: output/star/star/transcriptInfo.tab
      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
    - path: output/star/test.Aligned.out.bam
      md5sum: d85858bf55a523121dde762046a34c5c
    - path: output/star/test.Chimeric.out.junction
      md5sum: ae87d1a24180f5a35cf6b47fdfdd0539
    - path: output/star/test.Log.final.out
    - path: output/star/test.Log.out
    - path: output/star/test.Log.progress.out
    - path: output/star/test.SJ.out.tab

- name: star align test_star_alignment_single_end stub
  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config -stub-run
  tags:
    - star/align
    - star
  files:
    - path: output/star/test.Aligned.unsort.out.bam
    - path: output/star/test.Log.final.out
    - path: output/star/test.Log.out
    - path: output/star/test.Log.progress.out
    - path: output/star/test.Chimeric.out.junction
    - path: output/star/test.unmapped_1.fastq.gz
    - path: output/star/test.unmapped_2.fastq.gz
    - path: output/star/test.tab
    - path: output/star/test.out.sam