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Tests 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. |
|
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 |
|
| Single End Reads | Single End Reads | n/a |
|
Version History
Version 2 (latest) Created 30th Aug 2021 at 17:00 by Simone Leo
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Version 1 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo
No revision comments
Creators and Submitter
Views: 1512 Downloads: 401
Created: 30th Aug 2021 at 17:00
Last updated: 30th Aug 2021 at 17:00
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https://orcid.org/0000-0001-8271-5429
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