tower.yml

reports:
  "multiqc/multiqc_report.html":
    display: "MultiQC HTML report"
  "Phoenix_Summary.tsv":
    display: "PHoeNIx summary"
  "GRiPHin_Summary.tsv":
    display: "PHoeNIx additional summary with AMR gene coverage,%ID information."
  "*.synopsis":
    display: "Summary of stats for the an individual sample"
    mimeType: text/plain
  "*.tax":
    display: "Best taxonomy assignment from either Kraken2 or FastANI"
    mimeType: text/plain
  "**/qc_stats/*_raw_read_counts.txt":
    display: "Raw read stats."
  "**/qc_stats/*.bbduk.log":
    display: "BBDuk log from phiX and adapter removal."
  "**/qc_stats/*.fastp.html":
    display: "Output of fastp run on raw reads."
  "**/qc_stats/*_1_fastqc.html":
    display: "FastQC output of R1 trimmed reads."
  "**/qc_stats/*_2_fastqc.html":
    display: "FastQC output of R2 trimmed reads."
  "**/qc_stats/*_trimmed_read_counts.txt":
    display: "Trimmed and cleaned read stats."
  "**/assembly/*.spades.log":
    display: "Spades log"
  "**/assembly/*.bbmap_filtered.log":
    display: "BBmap log from filtering <500bp contigs"
  "**/mlst/*.tsv":
    display: "MLST"
  "**/quast/*_summary.tsv ":
    display: "Quast report"
  "**/kraken2_asmbld_weighted/*..kraken2_wtasmbld.top_kraken_hit.txt":
    display: "Best hit from kraken2 on weighted scaffolds"
  "**/kraken2_trimd/*..kraken2_trimd.top_kraken_hit.txt":
    display: "Best hit from kraken2 on trimmed reads"
  "**/ANI/*.fastANI.txt":
    display: "List of matches from FastANI. The top match information is the first line of the file."
  "**/AMRFinder/*_all_genes.tsv":
    display: "AMRFinder Output"
  "**/gamma_ar/*_ResGANNCBI_*_srst2.gamma":
    display: "GAMMA AR gene calls"
    mimeType: text/csv
  "**/gamma_hv/*_HyperVirulence_*.gamma":
    display: "GAMMA Hypervirulence calls"
    mimeType: text/csv
  "**/gamma_pf/*_PF-Replicons_*.gamma":
    display: "GAMMA identified plasmid indicators"
    mimeType: text/csv