Pipeline processes

Subcommands invoked as individual processes during JASEN pipeline execution.

concatenate-files

Merge multiple YAML files (e.g. versions.yml outputs from pipeline runs) into a single YAML file. Later files override keys from earlier files.

jasentool concatenate-files -i <FILE> [-i <FILE> ...] -o <FILE>

Argument	Required	Default	Description
-i/--input	Yes (multiple)	—	Input YAML file(s) to concatenate
-o/--output-file	Yes	—	Path to output YAML file

Example

jasentool concatenate-files \
  -i run1/versions.yml \
  -i run2/versions.yml \
  -o merged_versions.yml

count-reads

jasentool count-reads --fastq1 <FILE> [--fastq2 <FILE>] --output-file <FILE>
                      [--sample-id <ID>]

Argument	Required	Default	Description
--fastq1	Yes	—	Path to R1 FASTQ file
--fastq2	No	—	Path to R2 FASTQ file (paired-end)
-o/--output-file	Yes	—	Path to JSON output file
--sample-id	No	—	Sample ID

Example

jasentool count-reads \
  --fastq1 sample_R1.fastq.gz \
  --fastq2 sample_R2.fastq.gz \
  --output-file read_counts.json \
  --sample-id SAMPLE001

create-yaml

Create a YAML input file for Bonsai upload from sample metadata and analysis result file paths. Builds IGV annotation entries automatically from BAM/BAI, VCF, and BED inputs.

jasentool create-yaml --sample-id <ID> --sample-name <NAME> --groups <GROUP> [--groups ...] -o <FILE>
                      [analysis result options ...]

Required options

Argument	Description
--sample-id	Sample ID
--sample-name	Sample name
--groups	Sample group(s); repeat for multiple
-o/--output	Output YAML file path

Analysis result options (all optional, all accept a file path)

Argument	Description
--amrfinder	AMRFinder output
--chewbbaca	chewBBACA cgMLST output
--emmtyper	Emmtyper output
--gambitcore	GAMBIT core output
--kleborate	Kleborate output
--kleborate-hamronization	Kleborate hAMRonization output
--kraken	Kraken2 output
--mlst	MLST output
--mykrobe	Mykrobe output
--nanoplot	NanoPlot output
--nextflow-run-info	Nextflow run info JSON
--postalnqc	Post-alignment QC output (mutually exclusive with --samtools-bedcov/--samtools-stats)
--quast	QUAST output
--ref-genome-annotation	Reference genome annotation
--ref-genome-sequence	Reference genome FASTA
--resfinder	ResFinder output
--samtools	Samtools stats output
--samtools-bedcov	Samtools bedcov output (mutually exclusive with --postalnqc)
--samtools-stats	Samtools stats (detailed) output (mutually exclusive with --postalnqc)
--sccmec	SCCmec output
--serotypefinder	SerotypeFinder output
--shigapass	ShigaPass output
--ska-index	SKA index file
--sourmash-signature	Sourmash signature file
--spatyper	spaTyper output
--tbprofiler	TBProfiler output
--virulencefinder	VirulenceFinder output

IGV annotation options (all optional)

Argument	Description
--bam	BAM alignment file (creates IGV alignment track)
--bai	BAM index file
--vcf	VCF variant file (creates IGV variant track)
--tb-grading-rules-bed	TB grading rules BED file (creates IGV BED track)
--tbdb-bed	TB database BED file (creates IGV BED track)

Other options

Argument	Description
--lims-id	LIMS ID
--software-info	Software info file(s); repeat for multiple

Example

jasentool create-yaml \
  --sample-id SAMP001 \
  --sample-name "Sample 001" \
  --groups wgs \
  --bam aligned.bam \
  --bai aligned.bam.bai \
  --mlst mlst.json \
  --kraken kraken_report.txt \
  -o input.yml

annotate-delly

Annotate a Delly structural-variant VCF/BCF with gene and locus_tag INFO fields derived from a tabix-indexed BED file. Handles chromosome name mismatches between the VCF and BED (single-contig BED files are remapped automatically).

jasentool annotate-delly -v <VCF> -b <BED> -o <OUTPUT>

Argument	Required	Default	Description
-v/--vcf	Yes	—	Delly VCF/BCF to annotate
-b/--bed	Yes	—	Tabix-indexed BED file with gene annotations
-o/--output	Yes	—	Output annotated VCF path

Example

jasentool annotate-delly \
  -v delly.bcf \
  -b converged_who_fohm_tbdb.bed.gz \
  -o delly_annotated.vcf

create-blacklist

Build a minority variant blacklist by running samtools mpileup and minority base distribution analysis across a set of BAM files, then aggregating positions that exceed a frequency threshold in enough samples. The resulting TSV can be passed to minority-report via --blacklist to exclude known high-noise positions.

Intermediate per-sample mpileup and distribution files are written to --output-dir. Only samples whose stem matches --sample-pattern contribute to the final blacklist.

jasentool create-blacklist (--input-file <FILE> | --input-dir <DIR>)
                            --output-dir <DIR> -o <FILE>
                            [--bed-file <FILE>] [--samtools <PATH>]
                            [--sample-pattern <REGEX>]
                            [--min-freq <FLOAT>] [--min-count <INT>]

Argument	Required	Default	Description
-i/--input-file	Yes (or --input-dir)	—	Text file of BAM paths, one per line
--input-dir	Yes (or --input-file)	—	Directory containing *.bam files
--output-dir	Yes	—	Directory for intermediate files
-o/--output-file	Yes	—	Output blacklist TSV path
--bed-file	No	—	BED file passed to samtools mpileup -l
--samtools	No	samtools	Path or name of the samtools executable
--sample-pattern	No	.*	Regex to filter which sample names contribute to the blacklist
--min-freq	No	0.05	Minimum minority frequency to count a position
--min-count	No	5	Minimum number of samples a position must appear in

Example

# From a directory of BAM files, only including samples matching ^[0-9]{2}MT
jasentool create-blacklist \
  --input-dir /data/bams \
  --output-dir /data/blacklist_work \
  -o blacklist.tsv \
  --bed-file targets.bed \
  --sample-pattern '^[0-9]{2}MT'

minority-report

Compute minority base frequency distribution from a pre-computed samtools mpileup file. For each position with coverage between 30 and 100, the second-highest base count divided by coverage is recorded as the minority frequency. Outputs two files:

• <output> — one minority frequency per line (no position)

• <output>.withpos — tab-separated position\tminority_freq

jasentool minority-report --mpileup <FILE> -o <OUTPUT_STEM> [--blacklist <FILE>]

Argument	Required	Default	Description
--mpileup	Yes	—	Input mpileup file (.mpileup or .mpileup.gz)
-o/--output	Yes	—	Output path stem (no extension)
--blacklist	No	—	Blacklist TSV of positions to exclude (see create-blacklist)

Example

jasentool minority-report \
  --mpileup sample.mpileup.gz \
  --blacklist blacklist.tsv \
  -o sample_minority_dist

post-align-qc

jasentool post-align-qc --sample-id <ID> --bam-file <FILE> --output-file <FILE>
                         [--bed-file <FILE>] [--cpus <N>]

Argument	Required	Default	Description
--sample-id	Yes	—	Sample ID
--bam-file	Yes	—	Input BAM file
-o/--output-file	Yes	—	Path to QC JSON output file
--bed-file	No	—	Input BED file
--cpus	No	2	Number of CPUs

Example

jasentool post-align-qc \
  --sample-id SAMPLE001 \
  --bam-file aligned.bam \
  --output-file qc.json \
  --bed-file targets.bed \
  --cpus 4