Workflows
What is a Workflow?Filters
Type: Nextflow
Creators: Jasmin Frangenberg, Anan Ibrahim, James A. Fellows Yates
Submitter: WorkflowHub Bot
This workflow runs the FEELnc tool to annotate long non-coding RNAs. Before annotating these long non-coding RNAs, StringTie will be used to assemble the RNA-seq alignments into potential trancriptions. The gffread tool provides a genome annotation file in GTF format.
Decontamination Workflow
Decontamination (foreign contaminants and mitochondrial sequences) of genome assembly after scaffolding step. Part of the VGP Suite.
Inputs
- Genome Assembly [fasta]
- Database for Kraken2. Database containing the possible contaminants.
Ouput
- List of contaminant scaffolds
- List of mitochondrial scaffolds
- Decontaminated assembly
This workflow allows for genome annotation using Maker and evaluates the quality of the annotation.
B/T cell repertoire analysis pipeline with immcantation framework. WIP, currently requires a bunch of changes first.
Type: Nextflow
Creators: Gisela Gabernet, Simon Heumos, Alexander Peltzer
Submitter: WorkflowHub Bot
PISAD - Phsaed Intraspecies Sample Anomalies Detection tool
Summary
We developed PISAD, a tool designed to detect anomalies in cohort samples without requiring reference information. It is primarily divided into two stages. Stage 1: We select low-error data from the cohort and conduct reference-free SNP calling to construct a variant sketch. Stage 2: By comparing the k-mer counts of other cohort data to the variant sketch, we infer the relationships between the sample and other samples to ...
Type: Nextflow
Creators: Damon-Lee Pointon, Mahesh Panchel, Yumi Sims, Will Eagles, Matthieu Muffato, Solenne Correard, Josie Paris
Submitter: Damon-Lee Pointon
REFLOW is a workflow manager tool designed to streamline and automate tasks related to renewable energy potential analyses. It is built with Luigi and provides an automated, robust framework for data acquisition, processing, land/sea eligibility analysis, technology placements, simulations and visualizations. It is build with transparency and reproducibility in mind.