Assembly-Hifi-Trio-phasing-VGP5-tests.yml

- doc: Test outline for Assembly-Hifi-Trio-phasing-VGP5
  job:
    'Meryl Database : Child':
      class: File
      location: https://zenodo.org/records/10056319/files/Meryl%20Database%20-%20Child.meryldb?download=1
      filetype: meryldb
    'Hapmer Database : Paternal':
      class: File
      location: https://zenodo.org/records/10056319/files/Hapmer%20Database%20-%20Paternal.meryldb?download=1
      filetype: meryldb
    'Hapmer Database : Maternal':
      class: File
      location: https://zenodo.org/records/10056319/files/Hapmer%20Database%20-%20Maternal.meryldb?download=1
      filetype: meryldb
    Genomescope Summary:
      class: File
      location: https://zenodo.org/records/10056319/files/Genomescope%20Summary.txt?download=1
      filetype: txt
    Genomescope Model Parameters:
      class: File
      path: test-data/GenomeScope_Model_parameters.tabular
      filetype: tabular
    'Pacbio Reads Collection : child':
      class: Collection
      collection_type: list
      elements:
      - class: File
        identifier: yeast_reads_sub1.fastq.gz
        location: https://zenodo.org/records/10056319/files/Pacbio%20Reads%20Collection.fastq.gz?download=1
    Paternal Illumina reads (hap1):
      class: Collection
      collection_type: list
      elements:
      - class: File
        identifier: hap1_2.fq
        location: https://zenodo.org/records/10056319/files/Sub_hap1_2.fastqsanger?download=1
      - class: File
        identifier: hap1_1.fq
        location: https://zenodo.org/records/10056319/files/Sub_hap1_1.fastqsanger?download=1
    Maternal Illumina reads (hap2):
      class: Collection
      collection_type: list
      elements:
      - class: File
        identifier: hap2_2.fq
        location: https://zenodo.org/records/10056319/files/Sub_hap2_2.fastqsanger?download=1
      - class: File
        identifier: hap2_1.fq
        location: https://zenodo.org/records/10056319/files/Sub_hap2_1.fastqsanger?download=1
    SAK input file (Optional): null
    Homozygous Read Coverage: null
    Bits for bloom filter: 32
    Name for Haplotype 1: Hap1
    Name for Haplotype 2: Hap2
    Database for Busco Lineage: v5
    Lineage: vertebrata_odb10 
  outputs:
    Estimated Genome size: 2288021 
    Assembly statistics for Hap1 and Hap2:
      asserts:
        has_line:
          line: "# contigs	81	27"
    usable hap1 gfa:
      asserts:
        has_n_lines:
          n: 167
    Hifiasm Trio hap1:
      asserts:
        has_n_lines:
          n: 162
    Busco Summary Hap1:
      asserts:
        has_text:
          text: "C:1.2%[S:1.1%,D:0.0%],F:0.4%,M:98.4%"
    Nx Plot:
      asserts:
        has_size: 
          value : 65000
          delta: 5000
    No Sequence hap1 gfa:
      asserts:
        not_has_text:
          text: "GTCAAGGCGA"