reports:
  "**/qc_report/run_qc_report_*.txt":  
    display: "Run QC report"
  "**/qc/nanoplot/*_raw_NanoPlot-report.html":
    display: "NanoPlot report for raw reads"
  "**/qc/nanoplot/*_filtered_NanoPlot-report.html":
    display: "NanoPlot report for quality filtered reads"
  "**/preprocessing/chopper/*_chopper.log":
    display: "Chopper quality filtering log"
  "**/preprocessing/porechop/*_porechop.log":
    display: "Porechop adapter trimming log"
  "**/read_classification/kaiju/*_krona.html":
    display: "Krona output"
  "**/read_classification/kaiju/*_kaiju_summary.tsv":
    display: "Kaiju summary"
  "**/read_classification/kaiju/*_kaiju_summary_viral.tsv":
    display: "Kaiju viral summary"
  "**/read_classification/kaiju/*_kaiju_summary_viral_filtered.tsv":
    display: "Kaiju viral summary filtered"
  "**/read_classification/kraken/*kraken2":
    display: "Kraken2 summary"
  "**/read_classification/kraken/*_bracken_report.txt":
    display: "Bracken summary"
  "**/read_classification/kraken/*_bracken_report_viral.txt":
    display: "Bracken viral summary"
  "**/read_classification/kraken/*_bracken_report_viral_filtered.txt":
    display: "Bracken viral filtered summary"
  "**/read_classification/homology_search/*_blastn_top_hits.txt":
    display: "Blastn read search (all top hits)"
  "**/read_classification/homology_search/*_blastn_top_viral_hits.txt":
    display: "Blastn read search (all top viral hits)"
  "**/read_classification/homology_search/*_blastn_top_viral_spp_hits.txt":
    display: "Blastn read search (all top viral species hits)"
  "**/read_classification/homology_search/*_queryid_list_with_viral_match.txt":
    display: "Blastn read search summary table (read ids by query viral id)"
  "**/read_classification/homology_search/*_read_classification_viral_spp_abundance.txt":
    display: "Blastn read search viral abundance table (read count per viral species)"
  "**/assembly/*cutadapt.log":
    display: "Cutadapt log for final primer check on derived de-novo assembly"
  "**/assembly/*_filtered.fa":
    display: "Filtered novo assembly after final primer check"
  "**/assembly/canu/*_canu.log":
    display: "De novo assembly log (Canu)"
  "**/assembly/flye/*_flye.log":
    display: "De novo assembly log (Flye)"
  "**/assembly/flye/*_flye_assembly.fasta":
    display: "De novo assembly fasta file (Flye)"
  "**/assembly/canu/*_canu_assembly.fasta":
    display: "De novo assembly fasta file (Canu)"
  "**/assembly/blast_to_ref/*canu_assembly.txt":
    display: "Blastn search of Canu-derived contigs against reference"
  "**/assembly/blast_to_ref/*flye_assembly.txt":
    display: "Blastn search of Flye-derived contigs against reference"
  "**/assembly/blastn/*_blastn_top_hits.txt":
    display: "Blastn assembly search (all top hits)"
  "**/assembly/blastn/*_blastn_top_viral_hits.txt":
    display: "Blastn assembly search (all top viral hits)"
  "**/assembly/blastn/*_blastn_top_viral_spp_hits.txt":
    display: "Blastn assembly search (all top viral species hits)"
  "**/assembly/blastn/*_queryid_list_with_viral_match.txt":
    display: "Blastn assembly search summary table (cluster ids by query viral id)"
  "**/assembly/blastn/*_viral_spp_abundance.txt":
    display: "Blastn assembly search viral abundance table (cluster count per viral species)"
  "**/mapping/*_histogram":
    display: "Coverage histogram of mapped reads against reference"
  "**/mapping/*_coverage.txt":
    display: "Coverage statistics of mapped reads against reference"
  "**/mapping/*_medaka.annotated.vcf.gz":
    display: "Filtered VCF derived by medaka and corrected using bcftools"
  "**/mapping/*_medaka.consensus.fasta":
    display: "Final consensus derived by bcftools"
  "**/clustering/cap3/*_clustering.fasta":
    display: "Fasta file of assembled clusters (Rattle and CAP3)"
  "**/clustering/blastn/*_blastn_top_hits.txt":
    display: "Blastn cluster search (all top hits)"
  "**/clustering/blastn/*_blastn_top_viral_hits.txt":
    display: "Blastn cluster search (all top viral hits)"
  "**/clustering/blastn/*_blastn_top_viral_spp_hits.txt":
    display: "Blastn cluster search (all top viral species hits)"
  "**/clustering/blastn/*_queryid_list_with_viral_match.txt":
    display: "Blastn cluster search summary table (cluster ids by query viral id)"
  "**/clustering/blastn/*_viral_spp_abundance.txt":
    display: "Blastn cluster search viral abundance table (cluster count per viral species)"
  "**/clustering/rattle/*_rattle.fasta":
    display: "Fasta file with the clusters created by Rattle"
  "**/clustering/rattle/transcriptome.fq":
    display: "FASTQ file with the clusters created by Rattle"

