sra-manifest-to-concatenated-fastqs/main
View on GitHub
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Frozen
Tests This workflow takes as input a SRA_manifest from SRA Run Selector and will generate one fastq file or fastq pair of file for each experiment (concatenated multiple runs if necessary). Output will be relabelled to match the column specified by the user.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Column number with SRA ID | Column number with SRA ID | Column number in the SRA_manifest with SRA ID (usually 1) |
|
| Column number with final identifier | Column number with final identifier | Column number in the SRA_list with final identifier |
|
| SRA_manifest | SRA_manifest | Input tabular from SRA Run Selector or home made (First row needs to be a header) |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Set SRA column to 1 if at 0 | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 4 | Compute column expression | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 5 | Cut columns of interest | Cut1 |
| 6 | generate table for relabelling | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0 |
| 7 | Cut to get only SRA | Cut1 |
| 8 | split file to get one SRA per file + header | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1 |
| 9 | get Fastqs from SRA IDs | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1 |
| 10 | relabel pair collec to get SRA+sample | __RELABEL_FROM_FILE__ |
| 11 | relabel single collec to get SRA+sample | __RELABEL_FROM_FILE__ |
| 12 | Apply rules | __APPLY_RULES__ |
| 13 | Apply rules | __APPLY_RULES__ |
| 14 | Concatenate multiple datasets | toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.2 |
| 15 | Concatenate multiple datasets | toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| paired_output | paired_output | n/a |
|
| single_output | single_output | n/a |
|
Version History
v0.1 (earliest) Created 24th Oct 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1d4fb3d9
Creators and Submitter
License
Activity
Views: 5288 Downloads: 1285 Runs: 1
Created: 24th Oct 2023 at 03:01
TagsThis item has not yet been tagged.
AttributionsNone
Related items
Advanced Teams list for this Workflow with search and filtering
IWC - Intergalactic Workflow Commission
Space: This Team is not associated with a Space
Public web page: https://github.com/galaxyproject/iwc
