virprof/references.yml at master · seiboldlab/virprof · GitHub

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references:
  # Human reference used for read and contig filtering.
  hg38g:
    - url: http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.annotation.gtf.gz
      type: gtf
    - url: http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/GRCh38.primary_assembly.genome.fa.gz
      type: fasta
    - url: http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.transcripts.fa.gz
      type: tx.fasta
    - url: https://sourceforge.net/projects/rseqc/files/BED/Human_Homo_sapiens/hg38_GENCODE.v38.bed.gz
      type: bed

    - type: pipeline
      stages:
        - index_star
    - type: pipeline
      stages:
        - index_rsem
    - type: pipeline
      stages:
        - index_salmon_decoyG
    - type: pipeline
      stages:
        - index_bowtie2
    - type: pipeline
      stages:
        - index_blast
    - type: pipeline
      stages:
        - index_fasta
    - type: pipeline
      stages:
        - index_tx_fasta

  # Human reference for test data (contains only start of chr1)
  hg38gtest:
    - type: gtf
      url: test_data/test.gtf.gz
    - type: fasta
      url: test_data/test.fasta.gz
    - type: tx.fasta
      url: test_data/test.tx.fasta.gz
    - type: pipeline
      stages:
        - index_star
    - type: pipeline
      stages:
        - index_rsem
    - type: pipeline
      stages:
        - index_salmonG
    - type: pipeline
      stages:
        - index_bowtie2
    - type: pipeline
      stages:
        - index_blast

  mm39g:
    - url: http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M27/gencode.vM27.annotation.gtf.gz
      type: gtf
    - url: http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M27/GRCm39.primary_assembly.genome.fa.gz
      type: fasta
    - url: http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M27/gencode.vM27.transcripts.fa.gz
      type: tx.fasta
    - type: pipeline
      stages:
        - index_star
    - type: pipeline
      stages:
        - index_rsem
    - type: pipeline
      stages:
        - index_salmon_decoyG
    - type: pipeline
      stages:
        - index_bowtie2
    - type: pipeline
      stages:
        - index_blast
    - type: pipeline
      stages:
        - index_fasta
    - type: pipeline
      stages:
        - index_tx_fasta


  # NCBI Nucleotide database for Blast
  NT:
    - url: !workdir databases/nt
      type: path
      match:
        - (?P<sample>[^.]+)\.((nal|not|nto|ntf|nos|ndb)|[0-9]+\.(nin|nhr|nsq|nsd|nog))
        - (?P<sample>[^.]+)\.(ndb|nhr|nin|nog|nos|not|nsq|ntf|nto)

  # Subset of NT for testing
  NT_test:
    - url: test_data/nt_test.tar.bz2
      type: dir
      files: [nt.ndb, nt.nhr, nt.nin, nt.nog, nt.nos, nt.not, nt.nsq, nt.ntf, nt.nto]
      id: nt

  # NCBI Taxonomy dump for classification
  NcbiTaxonomy:
    - url: http://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
      type: archive
      files:
        ALL.NCBI.nodes.dmp: nodes.dmp
        ALL.NCBI.names.dmp: names.dmp
        ALL.NCBI.merged.dmp: merged.dmp
    - type: pipeline
      stages:
        - index_taxonomy_vp

  # VirusHostDB from genome.jp
  VHDB:
    - url: https://www.genome.jp/ftp/db/virushostdb/
      # or use ftp: - url: ftp://www.genome.jp/db/virushostdb/
      type: localdir
      files:
        virushostdb.tsv: virushostdb.tsv