ERGA ONT+Illumina Collapsed Purge+QC v2311 (WF3)
Version 1

Workflow Type: Galaxy
Work-in-progress

The workflow takes a trimmed Illumina WGS paired-end reads collection, Collapsed contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Collapsed contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

Inputs

ID Name Description Type
Estimated genome size #main/Estimated genome size n/a
  • File
GFA contigs #main/GFA contigs n/a
  • File
Meryl database #main/Meryl database n/a
  • File
ONT reads #main/ONT reads n/a
  • array containing
    • 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
7 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
8 Parse parameter value param_value_from_file
9 Parse parameter value param_value_from_file
10 Parse parameter value param_value_from_file
11 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
12 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
13 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
14 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
15 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
16 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
17 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
18 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
19 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
20 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3

Outputs

ID Name Description Type
output #main/output n/a
  • File

Version History

Version 1 (earliest) Created 9th Jan 2024 at 10:40 by Diego De Panis

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Views: 632

Created: 9th Jan 2024 at 10:40

Last updated: 9th Jan 2024 at 10:44

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