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. n/a

Steps

ID Name Description
0 Run accessions Text file containing run accessions (starting with SRR, ERR or DRR), one per line.
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
list_output_txt list_output_txt n/a
text_param text_param n/a
list_paired list_paired n/a
output_collection output_collection n/a
output_collection_other output_collection_other n/a
log log n/a
output output n/a
output output n/a
Total size: 28.9 KB
help Creators and Submitter
Creator
  • Marius van den Beek
Submitter
License
Activity

Views: 1017   Downloads: 9

Created: 23rd Jul 2021 at 10:18

Last updated: 21st Dec 2021 at 03:01

Last used: 23rd Jan 2022 at 08:41

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Version History

v0.1.2 (latest) 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

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