Purge-duplicates-one-haplotype-VGP6b/main

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Workflow Type: Galaxy

Purge contigs marked as duplicates by purge_dups in a single haplotype (could be haplotypic duplication or overlap duplication). If you think the purged contigs might belong to the other haplotype, use the workflow VGP6 instead. This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5).

SEEK ID: https://workflowhub.eu/workflows/751?version=14

Inputs

ID Name Description Type
Assembly Name Assembly Name For workflow report.
  • string
Assembly to leave alone (For Merqury comparison) Assembly to leave alone (For Merqury comparison) Assembly that does not need purging.
  • File
Assembly to purge Assembly to purge Assembly containing duplications to be purged.
  • File
Database for Busco Lineage Database for Busco Lineage Database to use for Busco lineages.
  • string
Estimated genome size - Parameter File Estimated genome size - Parameter File Estimated genome file obtained in the contiging workflow.
  • File
Genomescope model parameters Genomescope model parameters Model parameters obtained in the k-mer profiling workflow.
  • File
Haplotype Haplotype For workflow report.
  • string
Lineage Lineage Taxonomic lineage for the organism being assembled for Busco analysis
  • string
Meryl Database Meryl Database Meryl database obtained in the k-mer profiling workflow.
  • File
Name of purged assembly Name of purged assembly n/a
  • string?
Name of un-altered assembly Name of un-altered assembly n/a
  • string?
Pacbio Reads Collection - Trimmed Pacbio Reads Collection - Trimmed Trimmed PacBio HiFi reads—outputs of cutadapt in the contiging workflow.
  • File[]
Species Name Species Name For workflow report.
  • string

Steps

ID Name Description
13 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
14 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
15 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
16 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
17 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1
18 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
19 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
20 Estimated genome size param_value_from_file
21 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
22 Cut Cut1
23 Cut Cut1
24 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1
25 gfastats_data_prep n/a
26 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
27 Parse parameter value param_value_from_file
28 Parse parameter value param_value_from_file
29 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
30 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
31 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
32 Remove REPEATs from BED toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0
33 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
34 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
35 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
36 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
37 Convert purged fasta to gfa toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
38 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
39 compleasm toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy2
40 merqury_QV __EXTRACT_DATASET__
41 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
42 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
43 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
44 merqury_stats __EXTRACT_DATASET__
45 output_merqury.assembly_02.spectra-cn.fl __EXTRACT_DATASET__
46 gfastats_data_prep n/a
47 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
48 gfastats_plot n/a
49 Join two Datasets join1
50 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0
51 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0

Outputs

ID Name Description Type
Species for report Species for report n/a
  • File
Assembly for report Assembly for report n/a
  • File
Haplotype for report Haplotype for report n/a
  • File
Lineage for report Lineage for report n/a
  • File
Cutoffs Cutoffs n/a
  • File
Read Coverage and cutoffs calculation: Histogram plot Read Coverage and cutoffs calculation: Histogram plot n/a
  • File
Removed haplotigs Removed haplotigs n/a
  • File
Purged assembly Purged assembly n/a
  • File
qv_files qv_files n/a
  • File
Merqury on Phased assemblies: Images Merqury on Phased assemblies: Images n/a
  • File
Merqury on Phased assemblies: stats Merqury on Phased assemblies: stats n/a
  • File
Busco on Purged Primary assembly: short summary Busco on Purged Primary assembly: short summary n/a
  • File
Busco on Purged Primary assembly: summary image Busco on Purged Primary assembly: summary image n/a
  • File
Purged assembly (GFA) Purged assembly (GFA) n/a
  • File
Purged assembly statistics Purged assembly statistics n/a
  • File
Compleasm on purged Assembly: Full Table Busco Compleasm on purged Assembly: Full Table Busco n/a
  • File
Compleasm on purged Assembly: Full Table Compleasm on purged Assembly: Full Table n/a
  • File
Compleasm on purged Assembly: Miniprot Compleasm on purged Assembly: Miniprot n/a
  • File
Compleasm on purged Assembly: Translated Proteins Compleasm on purged Assembly: Translated Proteins n/a
  • File
merqury_QV merqury_QV n/a
  • File
output_merqury.spectra-cn.fl output_merqury.spectra-cn.fl n/a
  • File
output_merqury.spectra-asm.fl output_merqury.spectra-asm.fl n/a
  • File
output_merqury.assembly_01.spectra-cn.fl output_merqury.assembly_01.spectra-cn.fl n/a
  • File
merqury_stats merqury_stats n/a
  • File
output_merqury.assembly_02.spectra-cn.fl output_merqury.assembly_02.spectra-cn.fl n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot n/a
  • File
Assembly statistics for both assemblies Assembly statistics for both assemblies n/a
  • File
clean_stats clean_stats n/a
  • File

Version History

v0.8.0 (latest) Created 16th May 2025 at 03:02 by WorkflowHub Bot

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Frozen v0.8.0 cad66e1

v0.7.7 Created 15th May 2025 at 03:02 by WorkflowHub Bot

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v0.7.6 Created 2nd May 2025 at 03:02 by WorkflowHub Bot

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v0.7.5 Created 26th Mar 2025 at 11:59 by WorkflowHub Bot

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v0.7.4 Created 26th Mar 2025 at 11:59 by WorkflowHub Bot

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v0.7.3 Created 15th Feb 2025 at 03:02 by WorkflowHub Bot

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v0.1 (earliest) Created 15th Feb 2024 at 03:01 by WorkflowHub Bot

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Frozen v0.1 49773bd
help Creators and Submitter
Creators
Not specified
Additional credit

Galaxy, VGP

Submitter
Tools
Minimap2
purge_dups
gfastats
Merqury
BUSCO
compleasm
License
Creative Commons Attribution 4.0 International
Activity

Views: 6588   Downloads: 2089   Runs: 1

Created: 15th Feb 2024 at 03:01

Last updated: 16th May 2025 at 03:02

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