Workflows

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814 Workflows visible to you, out of a total of 888
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

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

Provenance generation when running SUNSET with Autosubmit
Work-in-progress

This workflow demonstrates the integration of FAIR principles into the workflow management ecosystem through provenance integration in Autosubmit, a workflow manager developed at the Barcelona Supercomputing Center (BSC), and SUNSET (SUbseasoNal to decadal climate forecast post-processing and aSSEssmenT suite), an R-based verification workflow also developed at BSC.

Autosubmit supports the generation of data provenance information based on RO-Crate, facilitating the creation of machine-actionable ...

Type: Autosubmit

Creator: Albert Puiggros

Submitter: Albert Puiggros

nf-core/pangenome

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

Type: Nextflow

Creators: Simon Heumos, Michael L Heuer

Submitter: WorkflowHub Bot

Laserfarm Jupyter Notebooks for Salisbury Plain
Stable

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 7.95 km2 large Salisbury Plain in the United Kingdom (1.866189 W, 51.220814 N). The work has been performed in the context of the EU project MAMBO (Modern Approaches to the Monitoring ...

Type: Jupyter

Creators: W. Daniel Kissling, Wessel Mulder, Jinhu Wang, Yifang Shi

Submitter: W. Daniel Kissling

DOI: 10.48546/workflowhub.workflow.1303.1

Laserfarm Jupyter Notebooks for Oostvaardersplassen
Stable

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 54 km2 large Oostvaardersplassen in the Netherlands (5.418842 E, 52.456870 N). The work has been performed in the context of the EU project MAMBO (Modern Approaches to the Monitoring ...

Type: Jupyter

Creators: W. Daniel Kissling, Wessel Mulder, Jinhu Wang, Yifang Shi

Submitter: W. Daniel Kissling

DOI: 10.48546/workflowhub.workflow.1302.1

Laserfarm Jupyter Notebooks for Monks Wood
Stable

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 0.08 km2 large Monks Wood in the United Kingdom (10.478393 E, 56.289050 N). The work has been performed in the context of the EU project MAMBO (Modern Approaches to the Monitoring ...

Type: Jupyter

Creators: W. Daniel Kissling, Wessel Mulder, Jinhu Wang, Yifang Shi

Submitter: W. Daniel Kissling

DOI: 10.48546/workflowhub.workflow.1301.1

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