Workflow Type: Galaxy
Frozen
Frozen
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 | gfastats_data_prep | n/a |
12 | Cut | Cut1 |
13 | Cut | Cut1 |
14 | Scatterplot with ggplot2 | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1 |
15 | 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 |
|
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
v0.1.4
d7dad7e
v0.1 (earliest) Created 4th Nov 2023 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
cdcc509
Creators and Submitter
Creators
Not specifiedAdditional credit
Galaxy, VGP
Submitter
Activity
Views: 3889 Downloads: 760 Runs: 0
Created: 4th Nov 2023 at 03:02
Last updated: 17th Aug 2024 at 03:02
Tags
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Attributions
None