Nextflow Registry | nf-core/stacks/refmap@0.0.0-6c4ed3a

nf-core/stacks/refmap @ 0.0.0-6c4ed3a

ref_map.pl script from Stacks for the analysis of RAD-seq data when a reference genome is available.

rad-seq gbs variant-calling population-genomics genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @TheGreatJack

Maintainers: @TheGreatJack

ref_map.pl script from Stacks for the analysis of RAD-seq data when a reference genome is available.

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

include { STACKS_REFMAP } from 'nf-core/stacks/refmap'

MIT License

Process

`Name`	`STACKS_REFMAP`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bams` file	BAM alignment files from individual samples `*.bam`

`popmap` file	Tab-delimited population map file `*.tsv`

Output 16 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`populations.snps.vcf` file	Stacks populations vcf output file `populations.snps.vcf`

#2 genepop tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`populations.snps.genepop` file	Stacks populations genepop output file `populations.snps.genepop`

#3 hapstats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`populations.hapstats.tsv` file	Stacks hapstats output file `populations.hapstats.tsv`

#4 sumstats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`populations.sumstats.tsv` file	Stacks populations sumstats output file `populations.sumstats.tsv`

#5 structure tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`populations.structure` file	Stacks populations structure output file `populations.structure`

#6 catalog_fa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`catalog.fa.gz` file	Stacks catalog fasta output file `catalog.fa.gz`

#7 haplotypes tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`populations.haplotypes.tsv` file	Stacks haplotypes output file `populations.haplotypes.tsv`

#8 gstacks_log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`gstacks.log` file	Stacks gstacks log output file `gstacks.log`

#9 ref_map_log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`ref_map.log` file	Stacks ref_map log output file `ref_map.log`

#10 catalog_chrs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`catalog.chrs.tsv` file	Stacks catalog chrs output file `catalog.chrs.tsv`

#11 catalog_calls tuple

`catalog.cal`
`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]