iwc/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6-tests.yml at 25e932fcb7ae932f041c48d378b4936bdcf9869b · galaxyproject/iwc · GitHub

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- doc: Test outline for Purge duplicate contigs from a diploid assembly VGP6
  job:
    Species Name: "Random Name"
    Assembly Name: "randName4"
    Hifiasm Primary assembly:
      class: File
      location: https://zenodo.org/records/10047837/files/Hifiasm%20Primary%20assembly.fasta?download=1
      filetype: fasta
      hashes:
      - hash_function: SHA-1
        hash_value: 0c2c964e5b5d8ca1025b6e9d8f24c8e2224e88c0
    Hifiasm Alternate assembly:
      class: File
      location: https://zenodo.org/records/10047837/files/Hifiasm%20Alternate%20assembly.fasta?download=1
      filetype: fasta
      hashes:
      - hash_function: SHA-1
        hash_value: bbf0d8abfb61a93c1641aa901ad2f347024cfadc
    Meryl Database:
      class: File
      location: https://zenodo.org/records/10047837/files/Meryl%20Database.meryldb?download=1
      filetype: meryldb
      hashes:
      - hash_function: SHA-1
        hash_value: d947eb6b317fcd30bc18e59f1ddd0afa52f72587
    Genomescope model parameters:
      class: File
      location: https://zenodo.org/records/10047837/files/Genomescope%20model%20parameters.tabular?download=1
      filetype: tabular
      hashes:
      - hash_function: SHA-1
        hash_value: 6daf4567ff37e9d5ceebf76ddeb15e0d5773f694
    Estimated genome size - Parameter File:
      class: File
      location: https://zenodo.org/records/10047837/files/Estimated%20genome%20size%20-%20Parameter%20File.expression.json?download=1
      filetype: expression.json
      hashes:
      - hash_function: SHA-1
        hash_value: 378f4f5733c91e6d6ea5be5b2b979ca865e78aae
    Pacbio Reads Collection - Trimmed:
      class: Collection
      collection_type: list
      elements:
      - class: File
        identifier: yeast_reads_sub1.fastq.gz
        location: https://zenodo.org/records/10047837/files/Pacbio%20Reads%20Collection%20-%20Trimmed_yeast_reads_sub1.fastq.gz.fastq.gz?download=1
        hashes:
        - hash_function: SHA-1
          hash_value: 22655cfeb863227dc07af755f6a892a4558c16cf
    Database for Busco Lineage: v5
    Lineage: vertebrata_odb10
    Name of primary assembly: Primary
    Name of alternate assembly: Alternate
    "What sequences are you purging?": "contig"
  outputs:
    Cutoffs for primary assembly:
      asserts:
        has_text:
          text: "1\t15\t15\t16\t16\t48"
    Purged Primary Assembly:
      decompress: true
      asserts:
        has_n_lines:
          n: 156
        has_text:
          text: "contig_1.pri"
    Purged Primary Assembly (gfa):
      asserts:
        has_n_lines:
          n: 157
    Cutoffs for alternate assembly:
      asserts:
        has_text:
          text: "1\t15\t15\t16\t16\t48"
    Purged Alternate Assembly:
      decompress: true
      asserts:
        has_n_lines:
          n: 144
        has_text:
          text: "contig_2.alt"
    Purged Alternate assembly (gfa):
      asserts:
        has_n_lines:
          n: 145
    Assembly statistics for purged assemblies:
      asserts:
        has_text:
          text: "# contigs\t78\t72"
    Nx Plot:
      asserts:
        has_size:
          value: 61000
          delta: 5000
    'Merqury on Phased assemblies: stats':
      element_tests:
        output_merqury.completeness:
          asserts:
            has_text:
              text: "both\tall\t1212740\t1300032\t93.2854"
    "Compleasm on purged primary/hap1 assembly: Translated Proteins":
      asserts:
        has_n_lines:
          n: 40390
    "Compleasm on purged alternate/hap2 assembly: Translated Proteins":
      asserts:
        has_n_lines:
          n: 40354
    Name mapping Alternate assembly:
      asserts:
        has_text:
          text: "h2tg000050l_path_1\tcontig_1.alt"
    Name mapping Hap1:
      asserts:
        has_text:
          text: "h1tg000055l_path_1\tcontig_1.pri"