modules/stacks_refmap

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

rad-seqgbsvariant-callingpopulation-genomicsgenomics

https://github.com/nf-core/modules/[...]/modules/nf-core/stacks/refmap

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`catalog_calls`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`catalog.calls`
`:file`

Stacks catalog calls output file

catalog.calls

`catalog_chrs`

`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

`catalog_fa`

`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

`gstacks_log`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`gstacks.log`
`:file`

Stacks gstacks log output file

gstacks.log

`gstacks_log_distribs`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`gstacks.log.distribs`
`:file`

Stacks gstacks log distribs output file

gstacks.log.distribs

`haplotypes`

`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

`hapstats`

`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

`sumstats`

`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

`sumstats_summary`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`populations.sumstats_summary.tsv`
`:file`

Stacks populations sumstats summary output file

populations.sumstats_summary.tsv

`populations_log`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`populations.log`
`:file`

Stacks populations log output file

populations.log

`populations_log_distribs`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`populations.log.distribs`
`:file`

Stacks populations log distribs output file

populations.log.distribs

`ref_map_log`

`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

`vcf`

`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

`genepop`

`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

`structure`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`populations.structure`
`:file`

Stacks populations structure output file

populations.structure

`versions_stacks_refmap`

`${task.process}`
`:string`

The name of the process

`stacks_refmap`
`:string`

The name of the tool

`populations -v 2>&1 | sed 's/^.* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`stacks_refmap`
`:string`

The name of the tool

`populations -v 2>&1 | sed 's/^.* //'`
`:eval`

The expression to obtain the version of the tool

Tools

stacks
GPL v3

Stacks is a software pipeline for building loci from short-read sequences.

catchenlab.life.illinois.edu/stacks catchenlab.life.illinois.edu/stacks/manual http://groups.google.com/group/stacks-users 10.1111/mec.12354

modules/stacks_refmap

Description

Input

meta :map

bams :file

popmap :file

Output

catalog_calls

meta :map

catalog.calls :file

catalog_chrs

meta :map

catalog.chrs.tsv :file

catalog_fa

meta :map

catalog.fa.gz :file

gstacks_log

meta :map

gstacks.log :file

gstacks_log_distribs

meta :map

gstacks.log.distribs :file

haplotypes

meta :map

populations.haplotypes.tsv :file

hapstats

meta :map

populations.hapstats.tsv :file

sumstats

meta :map

populations.sumstats.tsv :file

sumstats_summary

meta :map

populations.sumstats_summary.tsv :file

populations_log

meta :map

populations.log :file

populations_log_distribs

meta :map

populations.log.distribs :file

ref_map_log

meta :map

ref_map.log :file

vcf

meta :map

populations.snps.vcf :file

genepop

meta :map

populations.snps.genepop :file

structure

meta :map

populations.structure :file

versions_stacks_refmap

${task.process} :string

stacks_refmap :string

populations -v 2>&1 | sed 's/^.* //' :eval

Topics

versions

${task.process} :string

stacks_refmap :string

populations -v 2>&1 | sed 's/^.* //' :eval

Tools

stacksGPL v3

maintainer

get in touch

`meta`
`:map`

`bams`
`:file`

`popmap`
`:file`

`catalog_calls`

`meta`
`:map`

`catalog.calls`
`:file`

`catalog_chrs`

`meta`
`:map`

`catalog.chrs.tsv`
`:file`

`catalog_fa`

`meta`
`:map`

`catalog.fa.gz`
`:file`

`gstacks_log`

`meta`
`:map`

`gstacks.log`
`:file`

`gstacks_log_distribs`

`meta`
`:map`

`gstacks.log.distribs`
`:file`

`haplotypes`

`meta`
`:map`

`populations.haplotypes.tsv`
`:file`

`hapstats`

`meta`
`:map`

`populations.hapstats.tsv`
`:file`

`sumstats`

`meta`
`:map`

`populations.sumstats.tsv`
`:file`

`sumstats_summary`

`meta`
`:map`

`populations.sumstats_summary.tsv`
`:file`

`populations_log`

`meta`
`:map`

`populations.log`
`:file`

`populations_log_distribs`

`meta`
`:map`

`populations.log.distribs`
`:file`

`ref_map_log`

`meta`
`:map`

`ref_map.log`
`:file`

`vcf`

`meta`
`:map`

`populations.snps.vcf`
`:file`

`genepop`

`meta`
`:map`

`populations.snps.genepop`
`:file`

`structure`

`meta`
`:map`

`populations.structure`
`:file`

`versions_stacks_refmap`

`${task.process}`
`:string`

`stacks_refmap`
`:string`

`populations -v 2>&1 | sed 's/^.* //'`
`:eval`

`versions`

`${task.process}`
`:string`

`stacks_refmap`
`:string`

`populations -v 2>&1 | sed 's/^.* //'`
`:eval`

stacks
GPL v3