ERGA HiFi Hap1Hap2 Purge+QC v2309 (WF3)
Version 2

View on GitHub

Download RO Crate

Run on usegalaxy.eu

Workflow Type: Galaxy

Stable

The workflow takes a trimmed HiFi reads collection, Hap1/Hap2 contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Hap1 and Hap2 contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

SEEK ID: https://workflowhub.eu/workflows/606?version=2

DOI: 10.48546/workflowhub.workflow.606.2

Steps

ID	Name	Description
8	GFA to FASTA	toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
9	Parse parameter value	param_value_from_file
10	Parse parameter value	param_value_from_file
11	GFA to FASTA	toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
12	Parse parameter value	param_value_from_file
13	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
14	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
15	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
16	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
17	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
18	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
19	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
20	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
21	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
22	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
23	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
24	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
25	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
26	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
27	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
28	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
29	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
30	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
31	Merqury	toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3