Workflow Type: Galaxy

Parallel Accession Download

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession, and is therefore much faster and more robust to errors when many accessions need to be downloaded.

Inputs

ID Name Description Type
Run accessions 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/0.5.0
2 to parameter param_value_from_file
3 fasterq-dump toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0
4 flatten paired output __APPLY_RULES__
5 flatten single end output __APPLY_RULES__

Outputs

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

Version History

v0.1.6 (latest) 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

Marius van den Beek

Submitter
License
Activity

Views: 4672

Created: 23rd Jul 2021 at 10:18

Last updated: 6th Sep 2023 at 03:01

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