Workflows

What is a Workflow?
1342 Workflows visible to you, out of a total of 1435
Stable

Open in GitHub Codespaces GitHub Actions CI Status GitHub Actions Linting Status[![AWS ...

Type: Nextflow

Creators: Evangelos Karatzas, Martin Beracochea

Submitter: Evangelos Karatzas

DOI: 10.48546/workflowhub.workflow.1954.2

No description specified

Type: Galaxy

Creators: None

Submitter: ramiz khaled

No description specified

Type: Galaxy

Creators: None

Submitter: ramiz khaled

Work-in-progress

EOSC4Cancer_D2.2

Galaxy workflow used for EOSC4Cancer D2.2 - Analytical methods for data extraction, processing and sharing using biomedical images - demonstrator

An overview of the components for the image processing demonstrator can be seen in the diagram below diagram

Link to deliverable report on Zenodo: https://doi.org/10.5281/zenodo.15704480

Visualize and filter scATAC-seq anndata to produce a high quality count matrix

Associated Tutorial

This workflows is part of the tutorial Pre-processing of 10X Single-Cell ATAC-seq Datasets, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: GTN Bot

This workflow creates an count matrix anndata file given 10x scATAC-seq data.

Associated Tutorial

This workflows is part of the tutorial Pre-processing of 10X Single-Cell ATAC-seq Datasets, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: GTN Bot

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite with ...

Type: Nextflow

Creator: Andreas Wilm

Submitter: WorkflowHub Bot

Work-in-progress

pb_variants

A snakemake 9 based Pipeline for hifi snp, sv, cnv calling, phasing and more

Only PacBio data for now

!!THIS PIPLINE IS IN-DEVELOPMENT AND EXPERIMENTAL, USE AT YOUR OWN RISK!!

what this tool aims to deliver:

  • newest and best tools suited for HiFi data (only for now)
  • singletons and trio analysis (trio is coming sometime...)
  • human-first (hg38 for now), others should be possible (untested...)

included tools:

  • deepvariant or bcftools for snp calling
  • snps get used for ...

Type: Snakemake

Creators: None

Submitter: dan rick

Domestication of new parts and cloning simulation

Add new parts to your sequences before the cloning simulation and interact with the database.

input:

  • input: csv file (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.
  • JSON parameters file (optional) : The JSON file should contain the the parameters used in workflow tools. If this ...

Type: Galaxy

Creators: None

Submitter: ramiz khaled

Cloning simulation workflow for sequences present in DB

Run the GoldenGate cloning simulation for a list of constructs in a CSV file and interact with a database

inputs:

  • Assmbly Plan (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.
  • JSON parameters file (optional) : The JSON file should contain the the parameters used in workflow ...

Type: Galaxy

Creators: None

Submitter: ramiz khaled

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