Purge-duplicate-contigs-VGP6/main
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Workflow Type: Galaxy
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)
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Estimated genome size - Parameter File | Estimated genome size - Parameter File | n/a |
|
| Genomescope model parameters | Genomescope model parameters | n/a |
|
| Hifiasm Alternate assembly | Hifiasm Alternate assembly | n/a |
|
| Hifiasm Primary assembly | Hifiasm Primary assembly | n/a |
|
| Lineage | Lineage | Provide lineage for BUSCO (e.g., Vertebrata) |
|
| Meryl Database | Meryl Database | n/a |
|
| Name of alternate assembly | Name of alternate assembly | n/a |
|
| Name of primary assembly | Name of primary assembly | n/a |
|
| Pacbio Reads Collection - Trimmed | Pacbio Reads Collection - Trimmed | n/a |
|
| SAK input file | SAK input file | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+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/minimap2/2.26+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 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
| 24 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+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/minimap2/2.26+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/minimap2/2.26+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 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3 |
| 38 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 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 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Estimated Genome Size | Estimated Genome Size | n/a |
|
| Cutoffs for primary assembly | Cutoffs for primary assembly | n/a |
|
| Read Coverage and cutoffs calculation on primary assembly : Histogram plot | Read Coverage and cutoffs calculation on primary assembly : Histogram plot | n/a |
|
| Purged Primary Assembly | Purged Primary Assembly | n/a |
|
| Busco on Purged Primary assembly: short summary | Busco on Purged Primary assembly: short summary | n/a |
|
| Busco on Purged Primary assembly: summary image | Busco on Purged Primary assembly: summary image | n/a |
|
| Purged Primary Assembly (gfa) | Purged Primary Assembly (gfa) | n/a |
|
| Cutoffs for alternate assembly | Cutoffs for alternate assembly | n/a |
|
| Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot | Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot | n/a |
|
| Purged Alternate assembly | Purged Alternate assembly | n/a |
|
| Merqury on Phased assemblies: stats | Merqury on Phased assemblies: stats | n/a |
|
| Merqury on Phased assemblies: Images | Merqury on Phased assemblies: Images | n/a |
|
| Purged Alternate assembly (gfa) | Purged Alternate assembly (gfa) | n/a |
|
| Assembly stats on Primary and alternate assemblies | Assembly stats on Primary and alternate assemblies | n/a |
|
| Nx Plot | Nx Plot | n/a |
|
| Size Plot | Size Plot | n/a |
|
Version History
v0.1 (earliest) Created 31st Oct 2023 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1234270a
Creators and Submitter
Tools
Activity
Views: 6194 Downloads: 1605 Runs: 1
Created: 31st Oct 2023 at 03:02
Last updated: 17th Aug 2024 at 03:02
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