ERGA Long Reads PriAlt Purge+QC v2505 (WF3)
Version 1 (earliest)

Version 2 (latest)

Version 1 (earliest)

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Run on Galaxy

Workflow Type: Galaxy

Stable

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

SEEK ID: https://workflowhub.eu/workflows/1163?version=1

DOI: 10.48546/workflowhub.workflow.1163.1

Inputs

ID	Name	Description	Type
Alt GFA contigs	#main/Alt GFA contigs	n/a	File
Estimated genome size	#main/Estimated genome size	n/a	File
HiFi trimmed reads	#main/HiFi trimmed reads	n/a	array containing File
Meryl database	#main/Meryl database	n/a	File
Pri GFA contigs	#main/Pri GFA contigs	n/a	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
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/minimap2/2.28+galaxy0
15	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
16	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
17	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
18	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
19	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
20	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
21	Concatenate datasets	cat1
22	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0
23	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
24	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
25	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
26	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
27	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
28	Purge overlaps	toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
29	Merqury	toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
30	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
31	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
32	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0