ERGA HiC Hap1Hap2 Scaffolding+QC YaHS v2309 (WF4)
Version 1

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Run on Galaxy

Workflow Type: Galaxy

Stable

The workflow takes trimmed HiC forward and reverse reads, and Hap1/Hap2 assemblies to produce Hap1 and Hap2 scaffolded assemblies using YaHS. It also runs all the QC analyses (gfastats, BUSCO, Merqury and Pretext).

SEEK ID: https://workflowhub.eu/workflows/608?version=1

DOI: 10.48546/workflowhub.workflow.608.1

Inputs

ID	Name	Description	Type
Estimated genome size	Estimated genome size	n/a	File
Hap1 GFA	Hap1 GFA	gfa assembly file to scaffold	File
Hap2 GFA	Hap2 GFA	gfa assembly file to scaffold	File
HiC F trimmed	HiC F trimmed	HiC forward reads (already trimmed)	File
HiC R trimmed	HiC R trimmed	HiC reverse reads (already trimmed)	File
Meryl database	Meryl database	n/a	File
lineage	lineage	lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ...	string

Steps

ID	Name	Description
7	GFA to FASTA	toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
8	Parse parameter value	param_value_from_file
9	GFA to FASTA	toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
10	BWA-MEM2	toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
11	BWA-MEM2	toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
12	BWA-MEM2	toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
13	BWA-MEM2	toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
14	Filter and merge	toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
15	Filter and merge	toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
16	PretextMap	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0
17	YAHS	toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1
18	YAHS	toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1
19	PretextMap	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0
20	Pretext Snapshot	toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1
21	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
22	BWA-MEM2	toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
23	BWA-MEM2	toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
24	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
25	BWA-MEM2	toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
26	BWA-MEM2	toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
27	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
28	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
29	Merqury	toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
30	Pretext Snapshot	toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1
31	Filter and merge	toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
32	Filter and merge	toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
33	PretextMap	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0
34	PretextMap	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0
35	Pretext Snapshot	toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1
36	Pretext Snapshot	toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1

Outputs

ID	Name	Description	Type
_anonymous_output_1	_anonymous_output_1	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
_anonymous_output_3	_anonymous_output_3	n/a	File
_anonymous_output_4	_anonymous_output_4	n/a	File
_anonymous_output_5	_anonymous_output_5	n/a	File
_anonymous_output_6	_anonymous_output_6	n/a	File
_anonymous_output_7	_anonymous_output_7	n/a	File
_anonymous_output_8	_anonymous_output_8	n/a	File
_anonymous_output_9	_anonymous_output_9	n/a	File
_anonymous_output_10	_anonymous_output_10	n/a	File
_anonymous_output_11	_anonymous_output_11	n/a	File
_anonymous_output_12	_anonymous_output_12	n/a	File
_anonymous_output_13	_anonymous_output_13	n/a	File