vcf2lineage
1.0

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Workflow Type: Galaxy

workflow-automation

Associated Tutorial

This workflows is part of the tutorial vcf2lineage, available in the GTN

Thanks to...

Tutorial Author(s): Simon Bray, Wolfgang Maier

Workflow Author(s): Wolfgang Maier

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1293?version=1

Inputs

ID Name Description Type
Reference genome #main/Reference genome n/a
  • File
Variant calls #main/Variant calls n/a
  • array containing
    • File
min-AF for consensus variant #main/min-AF for consensus variant n/a
  • float

Steps

ID Name Description
3 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
4 SnpSift Filter toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
5 bcftools consensus toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10
6 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
7 Pangolin toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8

Outputs

ID Name Description Type
consensus #main/consensus n/a
  • File
consensus_variants #main/consensus_variants n/a
  • File
multisample_consensus_fasta #main/multisample_consensus_fasta n/a
  • File
pangolin_results #main/pangolin_results n/a
  • File

Version History

1.0 (earliest) Created 25th Jun 2024 at 11:20 by Helena Rasche

Added/updated 4 files


Open master 43ec935
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
BCFtools
pangolin
License
MIT License
Activity

Views: 146   Downloads: 41

Created: 25th Jun 2024 at 11:20

Last updated: 25th Jun 2024 at 11:20

help Attributions

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Total size: 78.1 KB
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