Workflow Type: Galaxy

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.

Inputs

ID Name Description Type
Run accessions #main/Run accessions Text file containing run accessions (starting with SRR, ERR or DRR), one per line.
  • File

Steps

ID Name Description
1 Split accessions to collection toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
2 fasterq-dump toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy0
3 flatten paired output __APPLY_RULES__
4 flatten single end output __APPLY_RULES__

Outputs

ID Name Description Type
Paired End Reads #main/Paired End Reads n/a
  • File
Single End Reads #main/Single End Reads n/a
  • File

Version History

v0.1.14 (latest) Created 11th Jun 2024 at 03:01 by WorkflowHub Bot

Updated to v0.1.14


Frozen v0.1.14 448a45c

v0.1.13 Created 23rd Apr 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.13


Frozen v0.1.13 a1cecd3

v0.1.6 Created 4th Oct 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.6


Frozen v0.1.6 136903d

v0.1.5 Created 13th Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.5


Frozen v0.1.5 e8be01c

v0.1.4 Created 6th Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.4


Frozen v0.1.4 6a7e27e

v0.1.3 Created 5th Feb 2022 at 03:00 by WorkflowHub Bot

Updated to v0.1.3


Frozen v0.1.3 7971b6d

v0.1.2 Created 21st Dec 2021 at 03:01 by WorkflowHub Bot

Updated to v0.1.2


Open master f932d31

v0.1.1 Created 27th Jul 2021 at 03:01 by WorkflowHub Bot

Updated to v0.1.1


Frozen master 2d827e0

v0.1 (earliest) Created 23rd Jul 2021 at 10:18 by WorkflowHub Bot

Added/updated 12 files


Frozen master ff682ec
help Creators and Submitter
Creator
  • Marius van den Beek
Additional credit

IWC

Submitter
License
Activity

Views: 5756   Downloads: 641

Created: 23rd Jul 2021 at 10:18

Last updated: 6th Sep 2023 at 03:01

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