- 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
          hashes:
          - hash_function: SHA-1
            hash_value: f60788cf7767330c960afb7ae6ba8f4009a11770
        - identifier: reverse
          class: File
          location: https://zenodo.org/record/6823059/files/Rep1_R2.fastq
          filetype: fastqsanger
          hashes:
          - hash_function: SHA-1
            hash_value: a0af1b73fa1b24d2abe5d816091f544133149b25
    adapter_forward: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
    adapter_reverse: 'GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'
    reference_genome: 'hg38canon'
    effective_genome_size: 2700000000
    normalize_profile: false
  outputs:
    Mapping stats:
      element_tests:
        Rep1:
          asserts:
            has_text:
              text: "289103 reads; of these:"
            has_text_matching:
              expression: "99.39% overall alignment rate"
    BAM filtered rmDup:
      element_tests:
        Rep1:
          asserts:
            has_size:
              value: 8661584
              delta: 800000
    MarkDuplicates metrics:
      element_tests:
        Rep1:
          asserts:
            has_text:
              text: "0.33"
    MACS2 summits:
      element_tests:
        Rep1:
          asserts:
            has_n_lines:
              n: 5870
    MACS2 narrowPeak:
      element_tests:
        Rep1:
          asserts:
            has_n_lines:
              n: 5870
    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: 238930"
- 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
          hashes:
          - hash_function: SHA-1
            hash_value: 78bc3a979ba69eb1e208fa1ef02cc4eaf2558204
        - identifier: reverse
          class: File
          path: test-data/SRR15904259_subset_reverse.fastqsanger.gz
          filetype: fastqsanger
          hashes:
          - hash_function: SHA-1
            hash_value: fc08c3fc612a5562566f5e7d987ebd89a6e3f43f
    adapter_forward: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
    adapter_reverse: 'GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'
    reference_genome: 'dm6'
    effective_genome_size: 120000000
    normalize_profile: true
  outputs:
    Mapping stats:
      element_tests:
        Rep1:
          asserts:
            has_text:
              text: "343237 reads; of these:"
            has_text_matching:
              expression: "98.17% 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: "0.001269"
    MACS2 summits:
      element_tests:
        Rep1:
          asserts:
            has_n_lines:
              n: 3231
    MACS2 narrowPeak:
      element_tests:
        Rep1:
          asserts:
            has_n_lines:
              n: 3231
    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: 489716"
    Coverage from MACS2 (bigwig):
      element_tests:
        Rep1:
          asserts:
            has_size:
              value: 5087932
              delta: 400000
