- doc: Test outline for CUT&RUN (hg38 bigwig conversion fails for memory issues)
  job:
    PE fastq input:
      class: Collection
      collection_type: list:paired
      elements:
      - class: Collection
        type: paired
        identifier: Rep1
        elements:
        - identifier: forward
          class: File
          location: https://zenodo.org/record/6823059/files/Rep1_R1.fastq
          filetype: fastqsanger
        - identifier: reverse
          class: File
          location: https://zenodo.org/record/6823059/files/Rep1_R2.fastq
          filetype: fastqsanger
    adapter_forward: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
    adapter_reverse: 'GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'
    reference_genome: 'hg38canon'
    effective_genome_size: 2700000000
  outputs:
    Mapping stats:
      element_tests:
        Rep1:
          asserts:
            has_text:
              text: "289103 reads; of these:"
            has_text_matching:
              expression: "99.31% overall alignment rate"
    BAM filtered rmDup:
      element_tests:
        Rep1:
          asserts:
            has_size:
              value: 10914132
              delta: 1000000
    MarkDuplicates metrics:
      element_tests:
        Rep1:
          asserts:
            has_text:
              text: "0.34"
    MACS2 summits:
      element_tests:
        Rep1:
          has_n_lines:
            n: 1856
    MACS2 narrowPeak:
      element_tests:
        Rep1:
          has_n_lines:
            n: 1856
    MACS2 peaks xls:
      element_tests:
        Rep1:
          asserts:
            has_text:
              text: "# tag size is determined as 40 bps"
            has_text_matching:
              expression: "# total tags in treatment: 383176"
- doc: Test outline for CUT&RUN (dm6)
  job:
    PE fastq input:
      class: Collection
      collection_type: list:paired
      elements:
      - class: Collection
        type: paired
        identifier: Rep1
        elements:
        - identifier: forward
          class: File
          path: test-data/SRR15904259_subset_forward.fastqsanger.gz
          filetype: fastqsanger
        - identifier: reverse
          class: File
          path: test-data/SRR15904259_subset_reverse.fastqsanger.gz
          filetype: fastqsanger
    adapter_forward: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
    adapter_reverse: 'GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'
    reference_genome: 'dm6'
    effective_genome_size: 120000000
  outputs:
    Mapping stats:
      element_tests:
        Rep1:
          asserts:
            has_text:
              text: "343237 reads; of these:"
            has_text_matching:
              expression: "98.03% overall alignment rate"
    BAM filtered rmDup:
      element_tests:
        Rep1:
          asserts:
            has_size:
              value: 18246620
              delta: 1000000
    MarkDuplicates metrics:
      element_tests:
        Rep1:
          asserts:
            has_text:
              text: "0.001264"
    MACS2 summits:
      element_tests:
        Rep1:
          has_n_lines:
            n: 3261
    MACS2 narrowPeak:
      element_tests:
        Rep1:
          has_n_lines:
            n: 3261
    MACS2 peaks xls:
      element_tests:
        Rep1:
          asserts:
            has_text:
              text: "# tag size is determined as 36 bps"
            has_text_matching:
              expression: "# total tags in treatment: 490492"
    Coverage from MACS2 (bigwig):
      element_tests:
        Rep1:
          asserts:
            has_size:
              value: 5087932
              delta: 400000
