- doc: Test outline for Ebola Virus Infection RNA-seq Analysis (A549 WT vs PTPN13-KO)
  job:
    reads_paired_collection:
      class: Collection
      collection_type: "list:paired"
      elements:
        - class: Collection
          collection_type: paired
          identifier: SRR5085167
          elements:
            - class: File
              identifier: forward
              path: test-data/SRR5085167_forward.fastqsanger.gz
            - class: File
              identifier: reverse
              path: test-data/SRR5085167_reverse.fastqsanger.gz
        - class: Collection
          collection_type: paired
          identifier: SRR5085168
          elements:
            - class: File
              identifier: forward
              path: test-data/SRR5085168_forward.fastqsanger.gz
            - class: File
              identifier: reverse
              path: test-data/SRR5085168_reverse.fastqsanger.gz
        - class: Collection
          collection_type: paired
          identifier: SRR5085169
          elements:
            - class: File
              identifier: forward
              path: test-data/SRR5085169_forward.fastqsanger.gz
            - class: File
              identifier: reverse
              path: test-data/SRR5085169_reverse.fastqsanger.gz
        - class: Collection
          collection_type: paired
          identifier: SRR5085170
          elements:
            - class: File
              identifier: forward
              path: test-data/SRR5085170_forward.fastqsanger.gz
            - class: File
              identifier: reverse
              path: test-data/SRR5085170_reverse.fastqsanger.gz
    salmon_index:
      class: File
      path: test-data/transcriptome.fasta
      filetype: fasta
    sample_metadata:
      class: File
      path: test-data/sample_metadata.tabular
      filetype: tabular
    tx2gene_map:
      class: File
      path: test-data/tx2gene.tabular
      filetype: tabular
  outputs:
    salmon_quant_collection:
      class: Collection
      element_tests:
        SRR5085167:
          asserts:
            has_text:
              text: "TX_02"
    deseq2_norm_counts:
      asserts:
        has_text:
          text: "GENE_02"
    deseq2_differential_results:
      asserts:
        has_text:
          text: "GENE_02"
    deseq2_plots:
      asserts:
        has_size:
          value: 1000
          delta: 1000000