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 |
|---|---|---|
val(meta), path(txt) |
tuple |
meta: Map containing sample information (must include 'id'); txt: Aggregated SvPileup output file |
Outputs
| Name | Type | Emit | Description |
|---|---|---|---|
val(meta), file("*_svpileup.aggregate.bedpe") |
tuple |
bedpe |
Tuple of meta and BEDPE format output file |
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 |
|---|---|---|
val(meta), path(bam), path(txt) |
tuple |
meta: Map containing sample information (must include 'id'); bam: Input BAM file; txt: SvPileup breakpoint output file |
Outputs
| Name | Type | Emit | Description |
|---|---|---|---|
val(meta), file("*_svpileup.aggregate.txt") |
tuple |
txt |
Tuple of meta and aggregated SvPileup output file |
COORDINATE_SORT
Defined in modules/coordinate_sort.nf:10
Sort a BAM file by genomic coordinates using samtools 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 |
Outputs
| Name | Type | Emit | Description |
|---|---|---|---|
val(meta), file("*_sorted.bam") |
tuple |
bam |
Tuple of meta and coordinate-sorted BAM file |
SV_PILEUP
Defined in modules/sv_pileup.nf:11
Detect structural variant evidence from a BAM file using fgsv SvPileup.
Inputs
| Name | Type | Description |
|---|---|---|
val(meta), path(bam) |
tuple |
meta: Map containing sample information (must include 'id'); bam: Input BAM file |
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 19:14:06 UTC.