hi-c-contact-map-for-assembly-manual-curation/main
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This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.
Steps
| ID | Name | Description |
|---|---|---|
| 11 | Hap2 not provided | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 12 | Add suffix to 2 haplotypes | n/a |
| 13 | concatenate HiFi | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2 |
| 14 | Add Suffix 1 haplotype | n/a |
| 15 | Pick Assembly | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 16 | Trim and Align Hi-C paired collection | n/a |
| 17 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 18 | seqtk_telo | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0 |
| 19 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
| 20 | PretextMap - Multimapping | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
| 21 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
| 22 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 23 | Cut | Cut1 |
| 24 | bamCoverage | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0 |
| 25 | bedtools Genome Coverage | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1 |
| 26 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 27 | Add Coverage Track - Multimapping | toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0 |
| 28 | Add Coverage Track | toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0 |
| 29 | Filter | Filter1 |
| 30 | Test if telomere track is empty | param_value_from_file |
| 31 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2 |
| 32 | False if telomere track is empty | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 33 | Add telomere track - Multimapping | toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0 |
| 34 | Add telomere track | toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0 |
| 35 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 36 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 37 | Add gaps track - Multimapping | toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0 |
| 38 | Add gaps track | toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0 |
| 39 | Add coverage gaps track - Multimapping | toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0 |
| 40 | Add coverage gaps track | toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0 |
| 41 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0 |
| 42 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0 |
| 43 | Extract dataset | __EXTRACT_DATASET__ |
| 44 | Extract dataset | __EXTRACT_DATASET__ |
Version History
v1.0beta6 (latest) Created 12th Jun 2025 at 03:01 by WorkflowHub Bot
Updated to v1.0beta6
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v1.0beta65b4be3e
v1.0beta5 Created 15th May 2025 at 03:03 by WorkflowHub Bot
Updated to v1.0beta5
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v1.0beta5
29022b1
v1.0beta4 Created 9th Apr 2025 at 03:01 by WorkflowHub Bot
Updated to v1.0beta4
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v1.0beta4
942f789
v1.0beta3 Created 8th Apr 2025 at 03:01 by WorkflowHub Bot
Updated to v1.0beta3
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v1.0beta3
22438d9
v1.0beta2 Created 29th Mar 2025 at 03:01 by WorkflowHub Bot
Updated to v1.0beta2
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v1.0beta2
7444f24
v1.0beta1 (earliest) Created 29th Mar 2025 at 03:01 by WorkflowHub Bot
Updated to v1.0beta1
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v1.0beta1
22269e3
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Activity
Views: 1068 Downloads: 296 Runs: 0
Created: 29th Mar 2025 at 03:01
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https://orcid.org/0000-0001-6421-3484
Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
Teams: Vertebrate Genomes Pipelines in Galaxy
Organizations: Galaxy
https://orcid.org/0000-0001-6421-3484
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IWC - Intergalactic Workflow Commission
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Public web page: https://github.com/galaxyproject/iwc
