Workflow Type: Galaxy
Stable

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

Inputs

ID Name Description Type
(Trimmed) Long Reads Collection #main/(Trimmed) Long Reads Collection Collection of Long reads in fastq format
  • array containing
    • File
Estimated genome size #main/Estimated genome size Select the est_genome_size result obtained during profiling
  • 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 Select the meryl_db result obtained during profiling
  • File
The Long Reads are PacBio HiFi #main/The Long Reads are PacBio HiFi If your long reads are HiFi, leave it 'yes'
  • boolean
The Long reads are ONT #main/The Long reads are ONT If your long reads are ONT, switch to 'yes'. IMPORTANT: Remember to also switch HiFi to 'no'
  • boolean
lineage #main/lineage lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ...
  • string
max depth #main/max depth Select the max_depth result obtained during profiling
  • File

Steps

ID Name Description
8 Parse parameter value param_value_from_file
9 Parse parameter value param_value_from_file
10 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0
11 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0
12 Bandage Pri (HiFi) toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
13 gfastats pri (HiFi) toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
14 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
15 Bandage alt toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
16 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
17 gfastats alt toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
18 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
19 Bandage Pri (ONT) toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
20 gfastats pri (ONT) toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
21 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
22 Bandage alt (ONT) toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
23 gfastats alt (ONT) toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
24 BUSCO pri (HiFi) toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
25 BUSCO alt (HiFi) toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
26 Merqury pri/alt (HiFi) toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
27 BUSCO pri (ONT) toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
28 Merqury pri/alt (ONT) toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
29 BUSCO alt (ONT) toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1

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_12 #main/_anonymous_output_12 n/a
  • File
_anonymous_output_13 #main/_anonymous_output_13 n/a
  • File
_anonymous_output_14 #main/_anonymous_output_14 n/a
  • File
_anonymous_output_15 #main/_anonymous_output_15 n/a
  • File
_anonymous_output_16 #main/_anonymous_output_16 n/a
  • File
_anonymous_output_17 #main/_anonymous_output_17 n/a
  • File
_anonymous_output_18 #main/_anonymous_output_18 n/a
  • File
_anonymous_output_19 #main/_anonymous_output_19 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_20 #main/_anonymous_output_20 n/a
  • File
_anonymous_output_21 #main/_anonymous_output_21 n/a
  • File
_anonymous_output_22 #main/_anonymous_output_22 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 2 (latest) Created 30th May 2025 at 13:52 by Diego De Panis

No revision comments

Open master fb422d4

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
License
Activity

Views: 2142   Downloads: 234   Runs: 59

Created: 24th Sep 2024 at 22:29

Last updated: 30th May 2025 at 13:55

Annotated Properties
Topic annotations
Operation annotations
help Attributions

None

Total size: 690 KB
Powered by
(v.1.17.0-main)
Copyright © 2008 - 2025 The University of Manchester and HITS gGmbH