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nf-core/nanomonsv/parse @ 0.0.0-6c4ed3a

Parse all the supporting reads of putative somatic SVs using nanomonsv. After successful completion, you will find supporting reads stratified by deletions, insertions, and rearrangements. A precursor to "nanomonsv get"

structural variants nanopore cancer genome somatic structural variations mobile element insertions long reads
Latest version: 0.0.0-6c4ed3a
Total downloads: 9
Source: nf-core/modules
Authors: @awgymer
Maintainers: @awgymer

Summary

Parse all the supporting reads of putative somatic SVs using nanomonsv. After successful completion, you will find supporting reads stratified by deletions, insertions, and rearrangements. A precursor to "nanomonsv get"

Get started

Add the following snippet to your workflow script to include this module.

include { NANOMONSV_PARSE } from 'nf-core/nanomonsv/parse'

License

MIT License

Process
Name NANOMONSV_PARSE
Input 1 channel
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
bam file

Aligned BAM file

 *.{bam}
bai file

BAM index file

 *.{bai}
Output 9 channels
#1 bp_info tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.bp_info.sorted.bed.gz file

Gzipped BED file containing breakpoint info

 *.{bed.gz}
#2 versions
versions.yml file

File containing software versions

 versions.yml
#3 deletions tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.deletion.sorted.bed.gz file

Gzipped BED file containing reads supporting deletions

 *.{bed.gz}
#4 insertions tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.insertion.sorted.bed.gz file

Gzipped BED file containing reads supporting insertions

 *.{bed.gz}
#5 bp_info_index tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.bp_info.sorted.bed.gz.tbi file

Index for gzipped BED file containing breakpoint info

 *.{bed.gz.tbi}
#6 rearrangements tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.rearrangement.sorted.bedpe.gz file

Gzipped BED file containing reads supporting rearrangements

 *.{bed.gz}
#7 deletions_index tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.deletion.sorted.bed.gz.tbi file

Index for gzipped BED file containing reads supporting deletions

 *.{bed.gz.tbi}
#8 insertions_index tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.insertion.sorted.bed.gz.tbi file

Index for gzipped BED file containing reads supporting insertions

 *.{bed.gz.tbi}
#9 rearrangements_index tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.rearrangement.sorted.bedpe.gz.tbi file

Index for gzipped BED file containing reads supporting rearrangements

 *.{bed.gz.tbi}
Tool Description Homepage
nanomonsv nanomonsv is a software for detecting somatic structural variations from paired (tumor and matched control) cancer genome sequence data. https://github.com/friend1ws/nanomonsv
Version 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:32:52 (UTC)