ERGA ONT+Illumina Collapsed Purge+QC v2311 (WF3)
Version 1

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Run on usegalaxy.eu

Workflow Type: Galaxy

Work-in-progress

The workflow takes a trimmed Illumina WGS paired-end reads collection, Collapsed contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Collapsed contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

SEEK ID: https://workflowhub.eu/workflows/701?version=1

Inputs

ID	Name	Description	Type
Estimated genome size	#main/Estimated genome size	n/a	File
GFA contigs	#main/GFA contigs	n/a	File
Meryl database	#main/Meryl database	n/a	File
ONT reads	#main/ONT reads	n/a	array containing File
Transition parameter	#main/Transition parameter	n/a	File
lineage	#main/lineage	lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ...	string
max depth	#main/max depth	n/a	File

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	Parse parameter value	param_value_from_file
10	Parse parameter value	param_value_from_file
11	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
12	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
13	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
14	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
15	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
16	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
17	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
18	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
19	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
20	Merqury	toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3