This is a Nextflow-based wrapper for the TBProfiler pipeline for antimicrobial resistance (AMR) analysis of whole-genome sequence data for Mycobacteria tuberculosis complex samples. This pipeline provides a convenient way to analyze many samples at once, on an HPC cluster system. It also integrates additional QC analysis of the input data using fastp, and of the generated alignments using Qualimap.
flowchart TD
reads --> fastp
fastp -- trimmed_reads --> tbprofiler
tbprofiler -- vcf --> snpit
tbprofiler -- bam --> qualimap_bamqc
nextflow run BCCDC-PHL/tbprofiler-nf \
--fastq_input <fastq_input_dir> \
--outdir <output_dir>
| Flag | Default Value | Description |
|---|---|---|
min_depth |
10 | Minimum depth of coverage used to call a SNP |
min_af_used_for_calling |
0.1 | Minimum minor allele fraction used to call a SNP |
min_af_used_for_prediction |
0.1 | Minimum minor allele fraction used to predict AMR |
An output directory will be created for each sample under the directory provided for the --outdir flag.
The following files will be produced for each sample:
.
└── sample-01
├── sample-01_TIMESTAMP_provenance.yml
├── sample-01_fastp.csv
├── sample-01_fastp.json
├── sample-01_qualimap_alignment_qc.csv
├── sample-01_snpit.tsv
├── sample-01_tbprofiler.bam
├── sample-01_tbprofiler.bam.bai
├── sample-01_tbprofiler_full_report.csv
├── sample-01_tbprofiler_full_report.json
├── sample-01_tbprofiler_lineage.csv
├── sample-01_tbprofiler_resistance.csv
├── sample-01_tbprofiler_summary.csv
├── sample-01_tbprofiler_targets.vcf
└── sample-01_tbprofiler_whole_genome.vcf