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Processes

This page documents all processes in the pipeline.

Contents

AGGREGATE_SV_PILEUP_TO_BEDPE

Defined in modules/aggregate_sv_pileup_to_bedpe.nf:11

Convert aggregated SvPileup output to BEDPE format using fgsv AggregateSvPileupToBedPE.

Inputs

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

Outputs

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

AGGREGATE_SV_PILEUP

Defined in modules/aggregate_sv_pileup.nf:12

Aggregate and merge pileups that are likely to support the same breakpoint using fgsv AggregateSvPileup.

Inputs

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

Outputs

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

COORDINATE_SORT

Defined in modules/coordinate_sort.nf:10

Sort a BAM file by genomic coordinates using samtools sort.

Inputs

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

Outputs

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

SV_PILEUP

Defined in modules/sv_pileup.nf:10

Detect structural variant evidence from a BAM file using fgsv SvPileup.

Inputs

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

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 18:53:33 UTC.