Workflows

What is a Workflow?
797 Workflows visible to you, out of a total of 870
DTC52 from Gitlab
Work-in-progress

CWL + RO-Crate Workflow Descriptions

This repository stores computational workflows described using the Common Workflow Language (CWL) and enriched with metadata using Research Object Crate (RO-Crate) conforming to the Workflow Run RO-Crate profile.

Each workflow is contained in its own directory (e.g., WF5201, WF6101, ...). Inside each workflow directory you will typically find at least:

  • The CWL workflow definition (with the same name as the directory, e.g., WF5201.cwl). ...

Type: Common Workflow Language

Creator: Marco Salvi

Submitter: Raül Sirvent

DTC61 from Gitlab
Work-in-progress

CWL + RO-Crate Workflow Descriptions

This repository stores computational workflows described using the Common Workflow Language (CWL) and enriched with metadata using Research Object Crate (RO-Crate) conforming to the Workflow Run RO-Crate profile.

Each workflow is contained in its own directory (e.g., WF5201, WF6101, ...). Inside each workflow directory you will typically find at least:

  • The CWL workflow definition (with the same name as the directory, e.g., WF5201.cwl). ...

Type: Common Workflow Language

Creator: Marco Salvi

Submitter: Raül Sirvent

tcga-data-nf
Work-in-progress

Workflow to download and prepare TCGA data.

The workflow divides the process of generating Gene Regulatory networks from TCGA cancer data in three steps:

  1. Downloading the raw data from GDC and saving the rds/tables needed later
  2. Preparing the data. This step includes filtering the data, normalizing it...
  3. Analysis of gene regulatory networks

Type: Nextflow

Creator: Viola Fanfani

Submitter: Viola Fanfani

PVGA

PVGA is a powerful virus-focused assembler that does both assembly and polishing. For virus genomes, small changes will lead to significant differences in terms of viral function and pathogenicity. Thus, for virus-focused assemblers, high-accuracy results are crucial. Our approach heavily depends on the input reads as evidence to produce the reported genome. It first adopts a reference genome to start with. We then align all the reads against the reference genome to get an alignment graph. After ...

Type: Python

Creators: None

Submitter: Zhi Song

Assembly-Hifi-Trio-phasing-VGP5/main

Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing

Inputs

  1. Hifi long reads [fastq]
  2. Concatenated Illumina reads : Paternal [fastq]
  3. Concatenated Illumina reads : Maternal [fastq]
  4. K-mer database [meryldb]
  5. Paternal hapmer database [meryldb]
  6. Maternal hapmer database [meryldb]
  7. Genome profile summary generated by Genomescope [txt]
  8. Genome model parameters generated by Genomescope [tabular]

...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Assembly-Hifi-only-VGP3/main

Contiging Solo:

Generate assembly based on PacBio Hifi Reads.

Inputs

  1. Hifi long reads [fastq]
  2. K-mer database [meryldb]
  3. Genome profile summary generated by Genomescope [txt]
  4. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate.
  5. Genomescope Model Parameters generated by Genomescope [tabular]
  6. Database for busco lineage (recommended: latest)
  7. Busco lineage (recommended: vertebrata)
  8. Name of first assembly
  9. Name of second ...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Purge-duplicates-one-haplotype-VGP6b/main

Purge duplicates from one haplotype. Prerequisites: run after a k-mer profiling workflow (VGP 1 or 2) and a contiging workflow (VGP 3,4 or 5).

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Purge-duplicate-contigs-VGP6/main

Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

nf-core/raredisease

GitHub Actions CI Status

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

Type: Nextflow

Creator: Clinical Genomics Stockholm

Submitter: WorkflowHub Bot

nf-core/mag

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

Type: Nextflow

Creators: No author provided, Hadrien Gourlé, Daniel Straub, Sabrina Krakau

Submitter: WorkflowHub Bot

Powered by
 (v.1.16.0-main)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH