ERGA HiC Collapsed Scaffolding+QC YaHS v2311 (WF4)
Version 1

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Run on usegalaxy.eu

Workflow Type: Galaxy

Work-in-progress

The workflow takes trimmed HiC forward and reverse reads, and one assembly (e.g.: Hap1 or Pri or Collapsed) to produce a scaffolded assembly using YaHS. It also runs all the QC analyses (gfastats, BUSCO, and Merqury).

SEEK ID: https://workflowhub.eu/workflows/702?version=1

Inputs

ID	Name	Description	Type
Estimated genome size	Estimated genome size	n/a	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
Purged GFA	Purged GFA	gfa assembly file to scaffold	File
lineage	lineage	lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ...	string

Steps

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