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nf-fgsv workflow parameters

Version: 0.1.0 ยท Nextflow workflow for running fgsv.

Inputs

Main workflow parameters

Name Description Type Default Required
--input Path to tab-separated file containing information about the samples in the experiment. string n/a yes

Workflows

Name Description Entry
(entry) n/a 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
val(meta), path(txt) tuple meta: Map containing sample information (must include 'id'); txt: Aggregated SvPileup output file

AGGREGATE_SV_PILEUP_TO_BEDPE Outputs

Name Type Emit Description
val(meta), file("*_svpileup.aggregate.bedpe") tuple bedpe Tuple of meta and BEDPE format output file

AGGREGATE_SV_PILEUP Inputs

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

AGGREGATE_SV_PILEUP Outputs

Name Type Emit Description
val(meta), file("*_svpileup.aggregate.txt") tuple txt Tuple of meta and aggregated SvPileup output file

COORDINATE_SORT Inputs

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

COORDINATE_SORT Outputs

Name Type Emit Description
val(meta), file("*_sorted.bam") tuple bam Tuple of meta and coordinate-sorted BAM file

SV_PILEUP Inputs

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

SV_PILEUP Outputs

Name Type Emit Description
val(meta), file("*_svpileup.txt") tuple txt Tuple of meta and SvPileup breakpoint output file
val(meta), file("*_svpileup.bam") tuple bam Tuple of meta and SvPileup BAM file

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.2.0 on 2026-03-03 22:49:08 UTC.