Purge-duplicates-one-haplotype-VGP6b/main

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Workflow Type: Galaxy

Purge duplicates from one haplotype. Prerequisites: run after a k-mer profiling workflow (VGP 1 or 2) and a contiging workflow (VGP 3,4 or 5).

SEEK ID: https://workflowhub.eu/workflows/751?version=8

Inputs

ID Name Description Type
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
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[]

Steps

ID Name Description
10 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
11 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
12 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
13 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
14 Estimated genome size param_value_from_file
15 Cut Cut1
16 Cut Cut1
17 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
18 gfastats_data_prep n/a
19 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
20 Parse parameter value param_value_from_file
21 Parse parameter value param_value_from_file
22 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
23 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
24 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
25 Remove REPEATs from BED toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
26 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
27 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
28 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
29 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0
30 Convert purged fasta to gfa toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
31 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
32 merqury_QV __EXTRACT_DATASET__
33 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
34 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
35 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
36 merqury_stats __EXTRACT_DATASET__
37 output_merqury.assembly_02.spectra-cn.fl __EXTRACT_DATASET__
38 gfastats_data_prep n/a
39 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
40 gfastats_plot n/a
41 Join two Datasets join1
42 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2
43 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1

Outputs

ID Name Description Type
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
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
qv_files qv_files n/a
  • File
Busco on Purged Primary assembly: summary image Busco on Purged Primary assembly: summary image n/a
  • File
Busco on Purged Primary assembly: short summary Busco on Purged Primary assembly: short summary n/a
  • File
Purged assembly (GFA) Purged assembly (GFA) n/a
  • File
Purged assembly statistics Purged assembly statistics 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

v0.7.2 (latest) Created 1st Feb 2025 at 03:01 by WorkflowHub Bot

Updated to v0.7.2


Frozen v0.7.2 b355196

v0.7.1 Created 7th Oct 2024 at 16:34 by WorkflowHub Bot

Updated to v0.7.1


Frozen v0.7.1 cfe3920

v0.7 Created 1st Aug 2024 at 03:02 by WorkflowHub Bot

Updated to v0.7


Frozen v0.7 8cac781

v0.6 Created 30th May 2024 at 11:36 by WorkflowHub Bot

Updated to v0.6


Frozen v0.6 d72d41d

v0.5 Created 23rd Apr 2024 at 03:01 by WorkflowHub Bot

Updated to v0.5


Frozen v0.5 47753b0

v0.4 Created 27th Mar 2024 at 03:02 by WorkflowHub Bot

Updated to v0.4


Frozen v0.4 32c3b9b

v0.3 Created 7th Mar 2024 at 03:02 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 31f46a9

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

Updated to v0.1


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

Galaxy, VGP

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

Views: 4187   Downloads: 1168   Runs: 0

Created: 15th Feb 2024 at 03:01

Last updated: 1st Feb 2025 at 03:01

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