Scaffolding-Bionano-VGP7/main
View on GitHub
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Frozen
Frozen
Tests Scaffolding with Bionano
Scaffolding using Bionano optical map data
Inputs
- Bionano data [cmap]
- Estimated genome size [txt]
- Phased assembly generated by Hifiasm [gfa1]
Outputs
- Scaffolds
- Non-scaffolded contigs
- QC: Assembly statistics
- QC: Nx plot
- QC: Size plot
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Bionano Data | Bionano Data | n/a |
|
| Conflict resolution files | Conflict resolution files | n/a |
|
| Estimated genome size - Parameter File | Estimated genome size - Parameter File | n/a |
|
| Input GFA | Input GFA | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Parse parameter value | param_value_from_file |
| 5 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 6 | Bionano Hybrid Scaffold | toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3 |
| 7 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 8 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 9 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 10 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 11 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
| 12 | gfastats_data_prep | n/a |
| 13 | Cut | Cut1 |
| 14 | Cut | Cut1 |
| 15 | Scatterplot with ggplot2 | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1 |
| 16 | Scatterplot with ggplot2 | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Scaffolds: agp | Scaffolds: agp | n/a |
|
| Bionano scaffolds reconciliated: gfa | Bionano scaffolds reconciliated: gfa | n/a |
|
| Bionano scaffolds reconciliated: fasta | Bionano scaffolds reconciliated: fasta | n/a |
|
| Assembly Statistics for s1 | Assembly Statistics for s1 | n/a |
|
| clean_stats | clean_stats | n/a |
|
| Nx Plot | Nx Plot | n/a |
|
| Size Plot | Size Plot | n/a |
|
Version History
v0.1.4 (latest) Created 7th Oct 2024 at 16:34 by WorkflowHub Bot
Updated to v0.1.4
Frozen
v0.1.4d7dad7e
v0.1 (earliest) Created 4th Nov 2023 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
cdcc509
Creators and Submitter
Activity
Views: 4158 Downloads: 803 Runs: 0
Created: 4th Nov 2023 at 03:02
Last updated: 17th Aug 2024 at 03:02
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
