Workflows
What is a Workflow?Filters
Pipeline to run and benchmark multiple sequence alignment tools.
Workflow for microbial (meta-)genome annotation
Input is a (meta)genome sequence in fasta format.
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bakta
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KoFamScan (optional)
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InterProScan (optional)
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eggNOG mapper (optional)
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To RDF conversion with SAPP (optional, default on) --> SAPP conversion Workflow in WorkflowHub
Workflow for converting (genome) annotation tool output into a GBOL RDF file (TTL/HDT) using SAPP
Current formats / tools:
- EMBL format
- InterProScan (JSON/TSV)
- eggNOG-mapper (TSV)
- KoFamScan (TSV)
git: https://gitlab.com/m-unlock/cwl
SAPP (Semantic Annotation Platform with Provenance):
https://gitlab.com/sapp
https://academic.oup.com/bioinformatics/article/34/8/1401/4653704
Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data and classify samples with pangolin and nextclade
This workflow takes a VCF dataset of variants produced by any of the *-variant-calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.
COVID-19: variation analysis on ARTIC PE data
The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...
Assembly of bacterial paired-end short read data with generation of quality metrics and reports
Type: Galaxy
Creators: Abromics , Pierre Marin, Clea Siguret, abromics-consortium
Submitter: WorkflowHub Bot
Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation
Type: Galaxy
Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium
Submitter: WorkflowHub Bot
Current version of this workflow: https://workflowhub.eu/workflows/1109. Please use only with the new version. KNIME workflow to gather ChEMBL permeability data is availbale: https://workflowhub.eu/workflows/1169.