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

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

Joint calling of structural variants from multiple samples using Sawfish

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @padraicc

Maintainers: @padraicc

Joint calling of structural variants from multiple samples using Sawfish

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

include { SAWFISH_JOINTCALL } from 'nf-core/sawfish/jointcall'

MIT License

Process

`Name`	`SAWFISH_JOINTCALL`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`sample_dirs` directory	Sample directories from sawfish discover step `*_discover_dir/`

#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 sample information e.g. [ id:'test' ]
`bams` file	Sorted BAM/CRAM file `*.{bam,cram}`
`bais` file	Index of BAM/CAM file `*.{bai,crai}`

#4 tuple

`meta4` map	Groovy Map containing additional information e.g. [ id:'csv' ]
`sample_csv` file	CSV file listing sample sawfish discover output and the sample bam file used with sawfish discover

Output 12 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*/contig.alignment.bam` file	Contig alignment BAM file `*.bam`

#2 log tuple

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

#3 tbi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`/_genotyped.sv.vcf.gz.tbi` file	Tabix index for the joint called VCF file `*_genotyped.sv.vcf.gz.tbi`

#4 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`/_genotyped.sv.vcf.gz` file	Joint called variants in compressed VCF format `*_genotyped.sv.vcf.gz`

#5 stats tuple

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

#6 maf_bw tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`/samples//maf.bw` file	Sample SNV MAF BigWig file `*.bw`

#7 depth_bw tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`/samples//depth.bw` file	Sample depth BigWig file `*.bw`

#8 bam_index tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*/contig.alignment.bam.csi` file	Contig alignment BAM index file `*.csi`