ERGA HiFi-only Assembly+QC Hifiasm v2409 (WF2)
Version 1

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Run on Galaxy

Workflow Type: Galaxy

Stable

The workflow takes a trimmed HiFi reads collection, and max coverage depth (calculated from WF1) to run Hifiasm in HiFi solo mode. It produces a Pri/Alt assembly, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

SEEK ID: https://workflowhub.eu/workflows/1162?version=1

DOI: 10.48546/workflowhub.workflow.1162.1

Inputs

ID	Name	Description	Type
Estimated genome size	#main/Estimated genome size	n/a	File
Hifiasm level of dups purging	#main/Hifiasm level of dups purging	0 to disable, 1 to only purge contained haplotigs, 2 to purge all types of haplotigs, 3 to purge all types of haplotigs in the most aggressive way. In default, 3 for non-trio assembly, 0 for trio-binning assembly. For trio-binning assembly, only level 0 and level 1 are allowed.	string
Meryl Database	#main/Meryl Database	n/a	File
Trimmed HiFi Reads Collection	#main/Trimmed HiFi Reads Collection	Collection of Long reads in fastq format.	array containing 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
6	Parse parameter value	param_value_from_file
7	Parse parameter value	param_value_from_file
8	Hifiasm	toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0
9	GFA to FASTA	toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
10	Bandage Pri	toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
11	gfastats pri	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.5+galaxy0
12	GFA to FASTA	toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
13	Bandage alt	toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
14	gfastats alt	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
15	BUSCO pri	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0
16	BUSCO alt	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0
17	Merqury pri/alt	toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4

Outputs

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