parallel-accession-download/main
View on GitHub
Download RO-Crate
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
No revision comments
Version 1 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo
No revision comments
Creators and Submitter
Views: 1510 Downloads: 400
Created: 30th Aug 2021 at 17:00
Last updated: 30th Aug 2021 at 17:00
TagsThis item has not yet been tagged.
AttributionsNone
Related items
https://orcid.org/0000-0001-8271-5429
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: Not specified
