Nextflow Registry | nf-core/sawfish/discover@0.0.0-6c4ed3a

nf-core/sawfish/discover @ 0.0.0-6c4ed3a

SV candidate discovery from PacBio HiFi data

sawfish structural-variant calling CNV calling Pacbio

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @padraicc

Maintainers: @padraicc

SV candidate discovery from PacBio HiFi data

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

include { SAWFISH_DISCOVER } from 'nf-core/sawfish/discover'

MIT License

Process

`Name`	`SAWFISH_DISCOVER`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`bam` file	Sorted BAM/CRAM file `*.{bam,cram}`
`bai` file	Index of BAM/CAM file `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'fasta' ]
`fasta` file	Reference genome in FASTA format `*.{fasta,fa}`

#3 tuple

`meta3` map	Groovy Map containing additional information e.g. [ id:'cn' ]
`expected_cn_bed` file	Expected copy number BED file `*.bed`

#4 tuple

`meta4` map	Groovy Map containing additional information e.g. [ id:'maf' ]
`maf_vcf` file	Variant file used to generate minor allele frequency track for this sample, in VCF or BCF format. `*.{vcf.gz,bcf.gz}`

#5 tuple

`meta5` map	Groovy Map containing additional information e.g. [ id:'cnv' ]
`cnv_exclude_regions_bed` file	BED file containing regions to exclude from CNV calling `*.bed`

Output 20 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`${prefix}/sawfish.log` file	Sawfish log file `*.log`

#2 maf_mpack tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`${prefix}/maf.mpack` file	MAF mpack file `*.mpack`

#3 max_depth tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`${prefix}/max.depth.bed` file	Max depth BED file `*.bed`

#4 run_stats tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`${prefix}/run.stats.json` file	Run statistics JSON file `*.json`

#5 depth_mpack tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`${prefix}/depth.mpack` file	Depth mpack file `*.mpack`

#6 expected_cn tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`${prefix}/expected.copy.number.bed` file	Expected copy number BED file `*.bed`

#7 discover_dir tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`${prefix}` directory	Directory containing all discover output files

#8 copynum_mpack tuple