Partial de novo workflow: c-s-g-pops only
v1.0

Workflow Type: Galaxy

workflow-partial-cstacks-sstacks-gstacks

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.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

This workflow takes in ustacks output, and runs cstacks, sstacks and gstacks.

To generate ustacks output see https://workflowhub.eu/workflows/349

For the full de novo workflow see https://workflowhub.eu/workflows/348

Inputs

ID Name Description Type
Population map Population map n/a
  • File
Ustacks inputs Ustacks inputs n/a
  • File[]

Steps

ID Name Description
2 Stacks2: cstacks toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.55+galaxy2
3 Stacks2: sstacks toolshed.g2.bx.psu.edu/repos/iuc/stacks2_sstacks/stacks2_sstacks/2.55+galaxy2
4 Stacks2: tsv2bam toolshed.g2.bx.psu.edu/repos/iuc/stacks2_tsv2bam/stacks2_tsv2bam/2.55+galaxy2
5 Stacks2: gstacks toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/2.55+galaxy2
6 Stacks2: populations toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.55+galaxy2

Outputs

ID Name Description Type
Stacks2: cstacks on input dataset(s) Catalog of loci Stacks2: cstacks on input dataset(s) Catalog of loci n/a
  • File
Stacks2: cstacks on input dataset(s) log file Stacks2: cstacks on input dataset(s) log file n/a
  • File
Stacks2: sstacks on input dataset(s) log file Stacks2: sstacks on input dataset(s) log file n/a
  • File
Stacks2: sstacks on input dataset(s) Matches to the catalog Stacks2: sstacks on input dataset(s) Matches to the catalog n/a
  • File
Stacks2: tsv2bam on input dataset(s) log file Stacks2: tsv2bam on input dataset(s) log file n/a
  • File
Stacks2: tsv2bam on input dataset(s) Matches to the catalog (bam) Stacks2: tsv2bam on input dataset(s) Matches to the catalog (bam) n/a
  • File
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_2 _anonymous_output_2 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_3 _anonymous_output_3 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
Stacks2: populations on input dataset(s) log file Stacks2: populations on input dataset(s) log file n/a
  • File
Haplotypes Stacks2: populations on input dataset(s) Raw Genotypes/Haplotypes 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_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 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
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File

Version History

v1.0 (earliest) Created 31st May 2022 at 08:56 by Anna Syme

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