BY-COVID: Data Download
1.0

Workflow Type: Galaxy

Downloads data from NCBI assuming the correct data input format. (I.e. it should be two columns, with a header, Run and Group, where Run is an SRR identifier.)

Associated Tutorial

This workflows is part of the tutorial BY-COVID: Data Download, available in the GTN

Features

Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): Marek Ostaszewski, Matti Hoch, Iacopo Cristoferi, Myrthe van Baardwijk, Saskia Hiltemann, Helena Rasche

Tutorial Contributor(s): Helena Rasche, Matti Hoch, Mira Kuntz, José Manuel Domínguez, Sanjay Kumar Srikakulam, Björn Grüning

Workflow Author(s): Helena Rasche

Funder(s): BeYond-COVID

SEEK ID: https://dev.workflowhub.eu/workflows/1330?version=1

Inputs

ID	Name	Description	Type
Sample Table	#main/Sample Table	This should be a two column sample table that looks like: ``` Run Group SRR16681566 healthy SRR16681565 healthy SRR16681564 healthy ```	File

Steps

ID	Name	Description
1	Cut	Cut1
2	Select	Grep1
3	Faster Download and Extract Reads in FASTQ	toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1

Outputs

ID	Name	Description	Type
output_collection	#main/output_collection	n/a	File

Version History

1.0 (earliest) Created 25th Jun 2024 at 11:25 by Helena Rasche

Added/updated 4 files

Open master 5b2db23

Creators and Submitter

Creators

Not specified

Submitter

Helena Rasche

Discussion Channel

GTN Matrix

Tool

SRA Software Toolkit

License

GNU Affero General Public License v3.0 or later

Activity

Views: 404 Downloads: 105

Created: 25th Jun 2024 at 11:25

Last updated: 25th Jun 2024 at 11:25

BY-COVID: Data Download 1.0