Partial de novo workflow: c-s-g-pops only
Version 1

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
Ustacks inputs Ustacks inputs n/a n/a
Population map Population map n/a n/a
input_stacks input_stacks runtime parameter for tool Stacks2: cstacks n/a
popmap popmap runtime parameter for tool Stacks2: cstacks n/a
popmap popmap runtime parameter for tool Stacks2: sstacks n/a
input_cat input_cat runtime parameter for tool Stacks2: tsv2bam n/a
input_matches input_matches runtime parameter for tool Stacks2: tsv2bam n/a
input_stacks input_stacks runtime parameter for tool Stacks2: tsv2bam n/a
input_type input_type runtime parameter for tool Stacks2: tsv2bam n/a
popmap popmap runtime parameter for tool Stacks2: tsv2bam n/a
kernel_smoothing kernel_smoothing runtime parameter for tool Stacks2: populations n/a
options_filtering options_filtering runtime parameter for tool Stacks2: populations n/a
options_filtering options_filtering runtime parameter for tool Stacks2: populations n/a

Steps

ID Name Description
0 Ustacks inputs
1 Population map
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
catalog catalog n/a
output_log output_log n/a
matches matches n/a
output_log output_log n/a
bams bams n/a
output_log output_log n/a
gstacks_out gstacks_out n/a
output_log output_log n/a
output_log output_log n/a
out_haplotypes out_haplotypes n/a
out_hapstats out_hapstats n/a
out_populations_log_distribs out_populations_log_distribs n/a
out_sumstats_sum out_sumstats_sum n/a
out_sumstats out_sumstats n/a
out_phistats out_phistats n/a
out_phistats_sum out_phistats_sum n/a
out_fststats_sum out_fststats_sum n/a
out_fasta_strict out_fasta_strict n/a
out_vcf_haplotypes_snps out_vcf_haplotypes_snps n/a
out_vcf_haplotypes_haps out_vcf_haplotypes_haps n/a
out_structure out_structure n/a

Version History

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

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Created: 31st May 2022 at 08:56

Last used: 6th Oct 2022 at 07:55

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