Partial ref-guided workflow - gstacks and pops
Version 1

Workflow Type: Galaxy

workflow-partial-gstacks-populations

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

This workflow is part of the reference-guided stacks workflow, https://workflowhub.eu/workflows/347

This workflow takes in bam files and a population map.

SEEK ID: https://workflowhub.eu/workflows/352?version=1

ID	Name	Description	Type
Bam files	Bam files	n/a	File[]
Population map	Population map	n/a	File

ID	Name	Description
2	Stacks2: gstacks	toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/2.55+galaxy2
3	Stacks2: populations	toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.55+galaxy2

ID	Name	Description	Type
Stacks2: gstacks on input dataset(s) Assembled contigs and variant sites	Stacks2: gstacks on input dataset(s) Assembled contigs and variant sites	n/a	File
Stacks2: gstacks on input dataset(s) log file	Stacks2: gstacks on input dataset(s) log file	n/a	File
_anonymous_output_1	_anonymous_output_1	n/a	File
Stacks2: populations on input dataset(s) Summary of Population-level summary statistics	Stacks2: populations on input dataset(s) Summary of Population-level summary statistics	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
_anonymous_output_3	_anonymous_output_3	n/a	File
Stacks2: populations on input dataset(s) log file	Stacks2: populations on input dataset(s) log file	n/a	File
Stacks2: populations on input dataset(s) Population-level haplotype summary statistics	Stacks2: populations on input dataset(s) Population-level haplotype summary statistics	n/a	File
Stacks2: populations on input dataset(s) Populations log distributions	Stacks2: populations on input dataset(s) Populations log distributions	n/a	File
_anonymous_output_4	_anonymous_output_4	n/a	File
Stacks2: populations on input dataset(s) Population-level summary statistics	Stacks2: populations on input dataset(s) Population-level summary statistics	n/a	File
_anonymous_output_5	_anonymous_output_5	n/a	File
_anonymous_output_6	_anonymous_output_6	n/a	File
Haplotypes	Stacks2: populations on input dataset(s) Raw Genotypes/Haplotypes	n/a	File
_anonymous_output_7	_anonymous_output_7	n/a	File