Workflow Type: Galaxy
Stable

The workflow takes a Long 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).

Inputs

ID Name Description Type
(Trimmed) Long Reads (Trimmed) Long Reads Collection of Long reads in fastq format
  • File[]
Alt Contigs GFA Alt Contigs GFA Alternate contigs in GFA format from the Hifiasm run results: alt_contigs_gfa
  • File
Estimated genome size Estimated genome size Select the est_genome_size result obtained during profiling
  • File
Meryl database Meryl database Select the meryl_db result obtained during profiling
  • File
Pri Contigs GFA Pri Contigs GFA Primary contigs in GFA format from the Hifiasm run results: pri_contigs_gfa
  • File
Transition parameter Transition parameter Select the transition_param result obtained during profiling
  • File
What type of Long Reads? What type of Long Reads? Select map-hifi if the long reads are PacBio HiFi (default), map-ont if the long reads are ONT
  • string
lineage lineage lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ...
  • string
max depth max depth Select the max_depth result obtained during profiling
  • File

Steps

ID Name Description
9 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
10 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
11 Parse parameter value param_value_from_file
12 Parse parameter value param_value_from_file
13 Parse parameter value param_value_from_file
14 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
15 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1
16 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1
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 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
20 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
21 Concatenate datasets cat1
22 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
23 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
24 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
25 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1
26 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1
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 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
30 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
31 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
32 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
33 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1

Version History

Version 2 (latest) Created 1st Jun 2025 at 12:24 by Diego De Panis

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Version 1 (earliest) Created 24th Sep 2024 at 22:44 by Diego De Panis

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Created: 24th Sep 2024 at 22:44

Last updated: 1st Jun 2025 at 12:25

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