tower.yml

reports:
  "**/multiqc/multiqc_report.html":
    display: "MultiQC HTML report"
  "**/Phoenix_Output_Report.tsv":
    display: "PHoeNIx output report"
  "**/*.synopsis":
    display: "Summary of stats for the an individual sample"
    mimeType: txt
  "**/*.tax":
    display: "Best taxonomy assignment from either Kraken2 or FastANI"
    mimeType: txt
  "**/**/mlst/*.tsv":
    display: "MLST"
  "**/**/quast/_report.tsv":
    display: "Quast report"
  "**/**/kraken2_asmbld_weighted/*.wtasmbld_summary.txt":
    display: "Best hit from kraken2 on weighted scaffolds"
  "**/**/kraken2_trimd/*.trimd_summary.txt":
    display: "Best hit from kraken2 on trimmed reads"
  "**/**/Assembly/*.spades.log":
    display: "Spades log"
    mimeType: txt
  "**/**/Assembly/*.bbmap_filtered.log":
    display: "BBmap log from filtering <500bp contigs"
    mimeType: txt
  "**/**/AMRFinder/*_all_genes.tsv":
    display: "AMRFinder Output"
  "**/**/gamma_ar/*_ResGANNCBI_*_srst2.gamma":
    display: "GAMMA AR gene calls"
    mimeType: tsv
  "**/**/gamma_hv/*_HyperVirulence_*.gamma":
    display: "GAMMA Hypervirulence calls"
    mimeType: tsv
  "**/**/gamma_pf/*_PF-Replicons_*.gamma":
    display: "GAMMA identified plasmid indicators"
    mimeType: tsv