Generated files

Other than the Snakemake report, this workflow keeps most intermediate files to allow the user to inspect any output as needed. More specifically, the results/{project} folder contains the following:

├── benchmarks
├── classification
│    └── {classifier}
│        └── {sample}
│           ├── {sample}_{marker}_kraken2.otumat
│           ├── {sample}_{marker}_kraken2.out
│           ├── {sample}_{marker}_kraken2.report
│           ├── {sample}_{marker}_kraken2.taxlist
│           └── {sample}_{marker}_kraken2.taxmat
├── itsx
│   ├── avg_seq_length.txt
│   ├── avg_seq_nr.txt
│   └── {sample}
│           ├── {sample}.graph
│           ├── {sample}.hmmer.table
│           ├── {sample}.{marker}.fasta
│           ├── {sample}_{marker}_final.fasta
│           ├── {sample}_no_detections.fasta
│           ├── {sample}_no_detections.txt
│           ├── {sample}.positions.txt
│           ├── {sample}.problematic.txt
│           └── {sample}.summary.txt
├── plotting
│   └── {marker}
│    │   └── {marker}_Barplot_{ra,counts}_{taxonomy}_rank.pdf
├── quality_checks
│    ├── 1_unfiltered
│    │   ├── nanostat
│    │   │   └── {sample}_unfiltered_stats.txt
│    │   └── pistis
│    |       └── {sample}.pdf
│    └── 2_filtered
│        ├── nanostat
│        │   └── {sample}_filtered_stats.txt
│        └── pistis
│            └── {sample}.pdf
├── reads
│    └── 2_qual_filtered_reads
│        ├── 1_porechop
│        |    └── {sample}.fastqc.gz
│        ├── 2_chopper
│        |    └── {sample}.fastqc.gz
│        └── 3_fasta
│            └── {sample}.fasta
└── tables
    ├── {marker}_otu_table_filtered.txt
    └── {marker}_otu_table.txt