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

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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

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

Version History

Version 1 (earliest) Created 24th Sep 2024 at 22:29 by Diego De Panis

Initial commit


Frozen Version-1 67e8dc7
help Creators and Submitter
Creator
Additional credit

ERGA

Submitter
Discussion Channel
https://github.com/ERGA-consortium/pipelines/discussions
Tools
Bandage
gfastats
BUSCO
Merqury
License
MIT License
Activity

Views: 315   Downloads: 29   Runs: 25

Created: 24th Sep 2024 at 22:29

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Total size: 409 KB
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