parallel-accession-download/main
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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
v0.1.14 (latest) Created 11th Jun 2024 at 03:01 by WorkflowHub Bot
Updated to v0.1.14
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v0.1.14448a45c
v0.1 (earliest) Created 23rd Jul 2021 at 10:18 by WorkflowHub Bot
Added/updated 12 files
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masterff682ec
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Views: 8001 Downloads: 1161 Runs: 0
Created: 23rd Jul 2021 at 10:18
Last updated: 6th Sep 2023 at 03:01
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