Workflows

What is a Workflow?
817 Workflows visible to you, out of a total of 891

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Type: Nextflow

Creators: @kbestak , @kbestak , @FloWuenne , @FloWuenne

Submitter: WorkflowHub Bot

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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.

Type: Galaxy

Creator: Romane Libouban

Submitter: WorkflowHub Bot

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

Type: Galaxy

Creator: Nadolina Brajuka

Submitter: WorkflowHub Bot

This workflow allows for genome annotation using Maker and evaluates the quality of the annotation.

Type: Galaxy

Creator: Romane Libouban

Submitter: WorkflowHub Bot

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: Argo Workflow

Creator: zhantian xu

Submitter: zhantian xu

DOI: 10.48546/workflowhub.workflow.1322.1

Work-in-progress

sanger-tol/curationpretext

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Type: Nextflow

Creators: Damon-Lee Pointon, Mahesh Panchel, Yumi Sims, Will Eagles, Matthieu Muffato, Solenne Correard, Josie Paris

Submitter: Damon-Lee Pointon

Work-in-progress

sanger-tol/curationpretext sanger-tol/curationpretext

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Type: Nextflow

Creators: Damon-Lee Pointon, Mahesh Panchel

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.

Type: Python

Creators: None

Submitter: Tristan Pelser

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