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nf-fgsv workflow parameters

Version: 0.1.0 · Nextflow workflow for running fgsv.

Inputs

Main workflow parameters

Name Description Type Default Required
--input Path to a tab-separated values (TSV) sample sheet describing the samples to analyze. The file must have a header row with the following required columns: - sample: a unique sample identifier containing no whitespace; used as the meta.id that names per-sample outputs. - bam: path to an existing BAM file for the sample (must end in .bam). See schemas/input_schema.json for the full validation rules. string n/a yes

Workflows

Name Description Entry
(entry) Detect structural-variant breakpoints from aligned reads using fgsv. The --input sample sheet provides one sample identifier and bam path per row (see the --input parameter for the full column specification). Every per-sample output — the sorted BAM, SvPileup BAM and text, aggregated breakpoints, and BEDPE — is published via the sample_outputs topic into a directory named after the sample's meta.id. For each sample the workflow runs: 1. COORDINATE_SORT — coordinate-sort the input BAM with samtools. 2. SV_PILEUP — gather read-level evidence for structural variants (fgsv SvPileup). 3. AGGREGATE_SV_PILEUP — merge pileups that likely support the same breakpoint. 4. AGGREGATE_SV_PILEUP_TO_BEDPE — convert the aggregated breakpoints to BEDPE. yes

Processes

Name Description
AGGREGATE_SV_PILEUP_TO_BEDPE Convert aggregated SvPileup output to BEDPE format using fgsv AggregateSvPileupToBedPE.
AGGREGATE_SV_PILEUP Aggregate and merge pileups that are likely to support the same breakpoint using fgsv AggregateSvPileup.
COORDINATE_SORT Sort a BAM file by genomic coordinates using samtools sort.
SV_PILEUP Detect structural variant evidence from a BAM file using fgsv SvPileup.

AGGREGATE_SV_PILEUP_TO_BEDPE Inputs

Name Type Description
meta val Map containing sample information (must include 'id')
txt path Aggregated SvPileup output file

AGGREGATE_SV_PILEUP_TO_BEDPE Outputs

Name Type Emit Description
meta: Map, bedpe: Path record bedpe Record of meta and the BEDPE format output file (bedpe)

AGGREGATE_SV_PILEUP Inputs

Name Type Description
meta val Map containing sample information (must include 'id')
bam path Input BAM file
txt path SvPileup breakpoint output file

AGGREGATE_SV_PILEUP Outputs

Name Type Emit Description
meta: Map, txt: Path record aggregated Record of meta and the aggregated SvPileup output file (txt)

COORDINATE_SORT Inputs

Name Type Description
meta val Map containing sample information (must include 'id')
bam path Input BAM file to be sorted

COORDINATE_SORT Outputs

Name Type Emit Description
meta: Map, bam: Path record sorted Record of meta and the coordinate-sorted BAM file (bam)

SV_PILEUP Inputs

Name Type Description
meta val Map containing sample information (must include 'id')
bam path Input BAM file

SV_PILEUP Outputs

Name Type Emit Description
meta: Map, bam: Path, txt: Path record result Record of meta, the SvPileup BAM file (bam), and the breakpoint output file (txt)

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.4.0 on 2026-06-03 18:53:48 UTC.