- name: Run star genomegenerate
  command: nextflow run ./tests/software/star -profile docker -entry test_star_genomegenerate -c tests/config/nextflow.config
  tags:
    - star
    - star_genomegenerate
  files:
    - path: output/star/star/Genome
      md5sum: 323c992bac354f93073ce0fc43f222f8
    - path: output/star/star/SA
      md5sum: 3e70e4fc6d031e1915bb510727f2c559
    - path: output/star/star/SAindex
      md5sum: a94198b95a245d4f64af2a7133b6ec7b
    - path: output/star/star/chrLength.txt
      md5sum: f2bea3725fe1c01420c57fb73bdeb31a
    - path: output/star/star/chrNameLength.txt
      md5sum: c7ceb0a8827b2ea91c386933bee48742
    - path: output/star/star/chrStart.txt
      md5sum: faf5c55020c99eceeef3e34188ac0d2f
    - path: output/star/star/exonGeTrInfo.tab
      md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
    - path: output/star/star/exonInfo.tab
      md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
    - path: output/star/star/genomeParameters.txt
      md5sum: ed47b8b034cae2fefcdb39321aea47cd
    - path: output/star/star/sjdbInfo.txt
      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
    - path: output/star/star/sjdbList.fromGTF.out.tab
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/star/star/sjdbList.out.tab
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/star/star/transcriptInfo.tab
      md5sum: 8fbe69abbbef4f89da3854873984dbac

- name: Run star single-end alignment
  command: nextflow run ./tests/software/star -profile docker -entry test_star_alignment_single_end -c tests/config/nextflow.config
  tags:
    - star
    - star_align
    - star_alignment_single_end
  files:
    - path: output/star/star/Genome
      md5sum: 323c992bac354f93073ce0fc43f222f8
    - path: output/star/star/SA
      md5sum: 3e70e4fc6d031e1915bb510727f2c559
    - path: output/star/star/SAindex
      md5sum: a94198b95a245d4f64af2a7133b6ec7b
    - path: output/star/star/chrLength.txt
      md5sum: f2bea3725fe1c01420c57fb73bdeb31a
    - path: output/star/star/chrNameLength.txt
      md5sum: c7ceb0a8827b2ea91c386933bee48742
    - path: output/star/star/chrStart.txt
      md5sum: faf5c55020c99eceeef3e34188ac0d2f
    - path: output/star/star/exonGeTrInfo.tab
      md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
    - path: output/star/star/exonInfo.tab
      md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
    - path: output/star/star/genomeParameters.txt
      md5sum: ed47b8b034cae2fefcdb39321aea47cd
    - path: output/star/star/sjdbInfo.txt
      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
    - path: output/star/star/sjdbList.fromGTF.out.tab
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/star/star/sjdbList.out.tab
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/star/star/transcriptInfo.tab
      md5sum: 8fbe69abbbef4f89da3854873984dbac
    - path: output/star/test.Aligned.out.bam
      md5sum: d7f59c1728482e76a18e3f6eb9c66c25
    - path: output/star/test.SJ.out.tab
      md5sum: d41d8cd98f00b204e9800998ecf8427e

- name: Run star paired-end alignment
  command: nextflow run ./tests/software/star -profile docker -entry test_star_alignment_paired_end -c tests/config/nextflow.config
  tags:
    - star
    - star_align
    - star_alignment_paired_end
  files:
    - path: output/star/star/Genome
      md5sum: 323c992bac354f93073ce0fc43f222f8
    - path: output/star/star/SA
      md5sum: 3e70e4fc6d031e1915bb510727f2c559
    - path: output/star/star/SAindex
      md5sum: a94198b95a245d4f64af2a7133b6ec7b
    - path: output/star/star/chrLength.txt
      md5sum: f2bea3725fe1c01420c57fb73bdeb31a
    - path: output/star/star/chrNameLength.txt
      md5sum: c7ceb0a8827b2ea91c386933bee48742
    - path: output/star/star/chrStart.txt
      md5sum: faf5c55020c99eceeef3e34188ac0d2f
    - path: output/star/star/exonGeTrInfo.tab
      md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
    - path: output/star/star/exonInfo.tab
      md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
    - path: output/star/star/genomeParameters.txt
      md5sum: ed47b8b034cae2fefcdb39321aea47cd
    - path: output/star/star/sjdbInfo.txt
      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
    - path: output/star/star/sjdbList.fromGTF.out.tab
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/star/star/sjdbList.out.tab
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/star/star/transcriptInfo.tab
      md5sum: 8fbe69abbbef4f89da3854873984dbac
    - path: output/star/test.Aligned.out.bam
      md5sum: 5c52bcaa15e86914ad6b895638235166
    - path: output/star/test.SJ.out.tab
      md5sum: d41d8cd98f00b204e9800998ecf8427e