iwc/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml at 3152c8c35e8b9653feb552ffeacba720dd96759e · jmchilton/iwc · GitHub

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- doc: Test outline for ChIPseq_SR
  job:
    SR fastq input:
      class: Collection
      collection_type: list
      elements:
      - identifier: wt_H3K4me3
        class: File
        location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read1.fastq.gz
        filetype: fastqsanger.gz
        hashes:
        - hash_function: SHA-1
          hash_value: 60cef994485a6bddf9e2b7efca464efc34559c12
    Adapter sequence: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
    Percentage of bad quality bases per read: 70
    Reference genome: 'mm10'
    Effective genome size: 1870000000
    Normalize profile: true
  outputs:
    MultiQC webpage:
      asserts:
      - that: "has_text"
        text: "wt_H3K4me3"
      - that: "has_text"
        text: <a href="#fastp" class="nav-l1">fastp</a>
      - that: "has_text"
        text: <a href="#bowtie2" class="nav-l1">Bowtie 2 / HiSAT2</a>
    'MultiQC on input dataset(s): Stats':
      asserts:
        has_line:
          line: "Sample\tmacs2-d\tmacs2-treatment_redundant_rate\tmacs2-peak_count\tbowtie_2_hisat2-overall_alignment_rate\tfastp-after_filtering_q30_rate\tfastp-after_filtering_q30_bases\tfastp-filtering_result_passed_filter_reads\tfastp-after_filtering_gc_content\tfastp-pct_surviving_reads\tfastp-pct_surviving_bases\tfastp-pct_adapter\tfastp-before_filtering_read1_mean_length"
        has_text_matching:
          expression: "wt_H3K4me3\t200.0\t0.0\t9\t98.[0-9]*\t93.[0-9]*\t2.3[0-9]*\t0.049[0-9]*\t57.[0-9]*\t99.[0-9]*\t99.[0-9]*\t0.12[0-9]*\t51.0"
    filtered BAM:
      class: Collection
      element_tests:
        wt_H3K4me3:
          asserts:
            has_size:
              value: 2587182
              delta: 200000
    MACS2 summits:
      class: Collection
      element_tests:
        wt_H3K4me3:
          asserts:
            has_n_lines:
              n: 9
    MACS2 peaks:
      class: Collection
      element_tests:
        wt_H3K4me3:
          asserts:
          - that: "has_text"
            text: "# effective genome size = 1.87e+09"
          - that: "has_text"
            text: "# d = 200"
          - that: "has_text"
            text: "# tags after filtering in treatment: 44528"
    MACS2 narrowPeak:
      class: Collection
      element_tests:
        wt_H3K4me3:
          asserts:
            has_n_lines:
              n: 9
    MACS2 report:
      class: Collection
      element_tests:
        wt_H3K4me3:
          asserts:
          - that: "has_text"
            text: "# effective genome size = 1.87e+09"
          - that: "has_text"
            text: "# d = 200"
          - that: "has_text"
            text: "# tags after filtering in treatment: 44528"
    coverage from MACS2:
      class: Collection
      element_tests:
        wt_H3K4me3:
          asserts:
            has_size:
              value: 563563
              delta: 10000
    mapping stats:
      class: Collection
      element_tests:
        wt_H3K4me3:
          asserts:
          - that: "has_text"
            text: "49813 reads; of these:"
          - that: "has_text"
            text: "44357 (89.05%) aligned exactly 1 time"
          - that: "has_text"
            text: "98.27% overall alignment rate"