sra-manifest-to-concatenated-fastqs/main
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Workflow Type: Galaxy
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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+galaxy1 |
| 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/3.1.0+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
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Created: 24th Oct 2023 at 03:01
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Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, iwc
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