hi-c-contact-map-for-assembly-manual-curation/main
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Workflow Type: Galaxy

Tests Not available

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.

SEEK ID: https://workflowhub.eu/workflows/1327?version=9

Steps

ID	Name	Description
21	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
22	Hap2 not provided	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
23	Add suffix to 2 haplotypes	n/a
24	Test if collection has only one item or is empty	n/a
25	Cutadapt	toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy1
26	Add Suffix 1 haplotype	n/a
27	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
28	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
29	Pick Assembly	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
30	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
31	Trim, Align, deduplicate Hi-C - Precuration	n/a
32	Teloscope	toolshed.g2.bx.psu.edu/repos/iuc/teloscope/teloscope/0.1.3+galaxy1
33	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1
34	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2
35	Gene Tracks for PretextMap	n/a
36	PretextMap	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0
37	PretextMap - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0
38	PretextMap - Multimapping low res	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0
39	PretextMap low res	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0
40	Select Q telomeres	Filter1
41	Select P telomeres	Filter1
42	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
43	Samtools merge	toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.22+galaxy1
44	Extract dataset	__EXTRACT_DATASET__
45	Pretext Snapshot	toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy1
46	Pretext Snapshot	toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy1
47	Q telomere bed	Cut1
48	P telomere bed	Cut1
49	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
50	Hifi Alignments	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
51	Extract dataset	__EXTRACT_DATASET__
52	Extract dataset	__EXTRACT_DATASET__
53	Test if Q telomere track is empty	param_value_from_file
54	Test if P telomere track is empty	param_value_from_file
55	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0
56	Samtools depth	toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.22+galaxy1
57	False if Q telomere track is empty	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
58	False if P telomere track is empty	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
59	Add Coverage Track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
60	Add Coverage Track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
61	Filter	Filter1
62	Add P telomere track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
63	Add P telomere track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
64	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
65	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
66	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
67	Cut	Cut1
68	Add Q telomere track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
69	Add Q telomere track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
70	bedtools MergeBED	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1+galaxy2
71	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
72	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
73	Add column	toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1
74	Add gaps track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
75	Add gaps track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
76	Add coverage gaps track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
77	Add coverage gaps track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
78	Add gene track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
79	Add genes track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
80	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
81	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0