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 |
|
Ustacks inputs | Ustacks inputs | n/a |
|
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 |
|
Stacks2: cstacks on input dataset(s) log file | Stacks2: cstacks on input dataset(s) log file | n/a |
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Stacks2: sstacks on input dataset(s) log file | Stacks2: sstacks on input dataset(s) log file | n/a |
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Stacks2: sstacks on input dataset(s) Matches to the catalog | Stacks2: sstacks on input dataset(s) Matches to the catalog | n/a |
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Stacks2: tsv2bam on input dataset(s) log file | Stacks2: tsv2bam on input dataset(s) log file | n/a |
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Stacks2: tsv2bam on input dataset(s) Matches to the catalog (bam) | Stacks2: tsv2bam on input dataset(s) Matches to the catalog (bam) | n/a |
|
Stacks2: gstacks on input dataset(s) Assembled contigs and variant sites | Stacks2: gstacks on input dataset(s) Assembled contigs and variant sites | n/a |
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Stacks2: gstacks on input dataset(s) log file | Stacks2: gstacks on input dataset(s) log file | n/a |
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_anonymous_output_2 | _anonymous_output_2 | n/a |
|
Stacks2: populations on input dataset(s) Populations log distributions | Stacks2: populations on input dataset(s) Populations log distributions | n/a |
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_anonymous_output_3 | _anonymous_output_3 | n/a |
|
_anonymous_output_4 | _anonymous_output_4 | n/a |
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Stacks2: populations on input dataset(s) Population-level summary statistics | Stacks2: populations on input dataset(s) Population-level summary statistics | n/a |
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Stacks2: populations on input dataset(s) log file | Stacks2: populations on input dataset(s) log file | n/a |
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Haplotypes | Stacks2: populations on input dataset(s) Raw Genotypes/Haplotypes | n/a |
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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 |
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_anonymous_output_5 | _anonymous_output_5 | n/a |
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_anonymous_output_6 | _anonymous_output_6 | n/a |
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Stacks2: populations on input dataset(s) Population-level haplotype summary statistics | Stacks2: populations on input dataset(s) Population-level haplotype summary statistics | n/a |
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_anonymous_output_7 | _anonymous_output_7 | n/a |
|
_anonymous_output_8 | _anonymous_output_8 | n/a |
|
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Views: 3795 Downloads: 217 Runs: 0
Created: 31st May 2022 at 08:56
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