Output Overview

You will get outputs that should look something like what's below. Please beaware, if you don't have all the outputs described that is OK, since some of the ouputs are dependent on the workflow used (e.g. clearlabs vs illumina_pe).

${OUTDIR}/${RUN_NAME}/
├── alignments
│   ├── ${SAMPLE_NAME}.{flagstat|stats}.txt
│   ├── ${SAMPLE_NAME}.{primertrim|primertrimmed.rg}.sorted.bam
│   └── ${SAMPLE_NAME}.{primertrim|primertrimmed.rg}.sorted.bam.bai
├── assemblies
│   └── ${SAMPLE_NAME}.{ivar|medaka}.consensus.fasta
├── cromwell
│   ├── ${SAMPLE_NAME}-metadata.json
│   └── ${SAMPLE_NAME}-std{err|out}.txt
├── dehosted_reads
│   └── ${SAMPLE_NAME}_R{1|2}_dehosted.fastq.gz
├── kraken2_reports
│   └── ${SAMPLE_NAME}_{dehosted_kraken2|kraken2}_report.txt
├── nextclade
│   └── ${SAMPLE_NAME}.{ivar|medaka}.consensus.nextclade.{auspice.json|json|tsv}
├── nf-info
│   ├── titan-{report|timeline}.html
│   └── titan-trace.txt
├── pangolin_reports
│   └── ${SAMPLE_NAME}.pangolin_report.csv
├── results
│   └── ${SAMPLE_NAME}.{json|tsv}
├── vadr_alerts
│   └── ${SAMPLE_NAME}.{ivar|medaka}.consensus.vadr.alt.list
├── titan-results.json
└── titan-results.tsv

Summary Results

These files are an aggregation of results into a single file.

Filename	Description
titan-results.json	A JSON (newline-delimited) summary of results for all samples
titan-results.tsv	A tab-delimited summary of results for all samples

Directory Description

alignments

${OUTDIR}/${RUN_NAME}/
└── alignments
    ├── ${SAMPLE_NAME}.{flagstat|stats}.txt
    ├── ${SAMPLE_NAME}.{primertrim|primertrimmed.rg}.sorted.bam
    └── ${SAMPLE_NAME}.{primertrim|primertrimmed.rg}.sorted.bam.bai

Extension	Description
.flagstat.txt	SAMtools flagstat quality metrics of the consensus BAM alignment
.sorted.bam	A BAM file of alignments created during consensus assembly
.sorted.bam.bai	An index of the BAM file
.stats.txt	SAMtools stats quality metrics of the consensus BAM alignment

assemblies

${OUTDIR}/${RUN_NAME}/
└── assemblies
    └── ${SAMPLE_NAME}.{ivar|medaka}.consensus.fasta

Extension	Description
.fasta	The final consensus assembly (ivar: illumina_pe, illumina_se; medaka: clearlabs, ont)

cromwell

${OUTDIR}/${RUN_NAME}/
└── cromwell
    ├── ${SAMPLE_NAME}-metadata.json
    └── ${SAMPLE_NAME}-std{err|out}.txt

Filename	Description
${SAMPLE_NAME}-metadata.json	A JSON format created by Cromwell which includes details about the run
${SAMPLE_NAME}-stderr.txt	A text file with error messages produced by Cromwell
${SAMPLE_NAME}-stdout.txt	A text file with log messages produced by Cromwell

dehosted_reads

${OUTDIR}/${RUN_NAME}/
└── dehosted_reads
    └── ${SAMPLE_NAME}_R{1|2}_dehosted.fastq.gz

Extension	Description
.fastq.gz	A set of reads that have had human-reads filtered out

kraken2_reports

${OUTDIR}/${RUN_NAME}/
└── kraken2_reports
    └── ${SAMPLE_NAME}_{dehosted_kraken2|kraken2}_report.txt

Extension	Description
dehosted_kraken2_report.txt	A Kraken2 report generated with the dehosted reads (e.g. human reads removed)
kraken2_report.txt	A Kraken2 report generated with the original reads

nextclade

${OUTDIR}/${RUN_NAME}/
└── nextclade
    └── ${SAMPLE_NAME}.{ivar|medaka}.consensus.nextclade.{auspice.json|json|tsv}

Extension	Description
auspice.json	A JSON file generated by Nextclade compatible with Auspice
.json	Output of Nextclade in JSON format
.txt	Output of Nextclade in tab-delimited format

nf-info

${OUTDIR}/${RUN_NAME}/
└── nf-info
    ├── titan-{report|timeline}.html
    └── titan-trace.txt

Filename	Description
titan-report.html	The Nextflow Execution Report
titan-timeline.html	The Nextflow Timeline Report
titan-trace.txt	The Nextflow Trace Report

pangolin_reports

${OUTDIR}/${RUN_NAME}/
└── pangolin_reports
    └── ${SAMPLE_NAME}.pangolin_report.csv

Extension	Description
.csv	The final lineage report generated by Pangolin for each sample

results

${OUTDIR}/${RUN_NAME}/
└── results
    └── ${SAMPLE_NAME}.{json|tsv}

Extension	Description
.json	A JSON (newline-delimited) summary of results for each samples
.tsv	A tab-delimited summary of results for each samples

vadr_alerts

${OUTDIR}/${RUN_NAME}/
└── vadr_alerts
    └── ${SAMPLE_NAME}.{ivar|medaka}.consensus.vadr.alt.list

Extension	Description
.list	A list of VADR alerts (if any) associated with a sample (ivar: illumina_pe, illumina_se; medaka: clearlabs, ont)

That should be it as far as output files go! If I missed one let me know!