metadata-and-sequences-from-bioproject-ids/main
v0.1

View on GitHub Download RO-Crate
Workflow Type: Galaxy

This workflow performs retrieval of SRA metadata tables and FASTQ sequence files from input BioProject IDs.

SEEK ID: https://workflowhub.eu/workflows/2214?version=1

Inputs

ID Name Description Type
BioProject IDs #main/BioProject IDs Column reporting BioProject IDs to recover
  • File
Display detailed metadata table #main/Display detailed metadata table Enable it to display detailed metadata table
  • boolean
Expand sample attributes in metadata #main/Expand sample attributes in metadata Enable it to expand sample_attribute
  • boolean
Include assay type in metadata #main/Include assay type in metadata Enable it to include assay type in output
  • boolean
Include sample attributes in metadata #main/Include sample attributes in metadata Enable it to include sample_attribute
  • boolean

Steps

ID Name Description
5 Separate BioProject IDs From each row a BioProject ID will be input in the next step toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
6 Relabel the separated BioProject IDs __RELABEL_FROM_FILE__
7 Add BioProject IDs as parameters BioProject IDs will be furnished as parameters to the pysradb tool param_value_from_file
8 Metadata From BioProject IDs This Step is useful to retrieve SRA table metadata for input BioProject IDs toolshed.g2.bx.psu.edu/repos/iuc/pysradb_search/pysradb_search/2.5.1+galaxy0
9 Get run_acccession per project toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3
10 Generate a single list toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3
11 Parallel Accession Download n/a

Outputs

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

Version History

v0.1 (earliest) Created 4th Jul 2026 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 13f43bc
help Creators and Submitter
Creators
Submitter
License
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Activity

Views: 13   Downloads: 1   Runs: 0

Created: 4th Jul 2026 at 03:01

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 69.9 KB
Powered by
 (v.1.18.0)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2026 The University of Manchester and HITS gGmbH