Purge-duplicate-contigs-VGP6/main
View on GitHub
Download RO Crate
Run on usegalaxy.eu
Workflow Type: Galaxy
Frozen
Frozen
Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)
Steps
| ID | Name | Description |
|---|---|---|
| 10 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 |
| 11 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 12 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 13 | Estimated genome size | param_value_from_file |
| 14 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 |
| 15 | Cut | Cut1 |
| 16 | Cut | Cut1 |
| 17 | Parse parameter value | param_value_from_file |
| 18 | Parse parameter value | param_value_from_file |
| 19 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 20 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 21 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 22 | Concatenate datasets | cat1 |
| 23 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 24 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0 |
| 25 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 26 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 27 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 |
| 28 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 29 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 30 | gfastats_data_prep | n/a |
| 31 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 32 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 |
| 33 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 34 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 35 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 36 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 37 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 38 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2 |
| 39 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 40 | gfastats_data_prep | n/a |
| 41 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
| 42 | gfastats_plot | n/a |
Version History
v0.3.8 (latest) Created 30th Apr 2024 at 03:02 by WorkflowHub Bot
Updated to v0.3.8
Frozen
v0.3.8511145a
v0.1 (earliest) Created 31st Oct 2023 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
234270a
Creators and SubmitterTools
License
Activity
Views: 2434
Created: 31st Oct 2023 at 03:02
Last updated: 30th Apr 2024 at 03:02
Tags AttributionsNone
Related items
Advanced People list for this Workflow with search and filtering
Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, iwc
Organizations: Bots, European Galaxy Team
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
