Purge-duplicate-contigs-VGP6/main

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Workflow Type: Galaxy

Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). 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/633?version=9

Inputs

ID Name Description Type
Estimated genome size - Parameter File Estimated genome size - Parameter File Estimated genome size generated by contiging workflows.
  • File
Genomescope model parameters Genomescope model parameters GenomeScope model parameters generated by K-mer profiling workflow.
  • File
Hifiasm Alternate assembly Hifiasm Alternate assembly Alternate assembly generated by contiging workflow in fasta format.
  • File
Hifiasm Primary assembly Hifiasm Primary assembly Primary assembly generated by contiging workflow in fasta format.
  • File
Lineage Lineage Taxonomic lineage for the organism being assembled for Busco analysis.
  • string
Meryl Database Meryl Database Meryl database generated by K-mer profiling workflow.
  • File
Name of alternate assembly Name of alternate assembly n/a
  • string?
Name of primary assembly Name of primary assembly n/a
  • string?
Pacbio Reads Collection - Trimmed Pacbio Reads Collection - Trimmed A simple list containing PacBio data in either fasta or fastq formats with trimmed adapters. These are usually generated by contiging workflows and have tag "trimmed_hifi" associated with them.
  • File[]
SAK input file SAK input file n/a
  • File?

Steps

ID Name Description
10 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
11 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
12 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
13 Estimated genome size param_value_from_file
14 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
15 Cut Cut1
16 Cut Cut1
17 Parse parameter value param_value_from_file
18 Parse parameter value param_value_from_file
19 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
20 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
21 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
22 Concatenate datasets cat1
23 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
24 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
25 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
26 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
27 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
28 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
29 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
30 gfastats_data_prep n/a
31 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
32 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
33 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
34 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
35 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
36 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
37 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
38 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
39 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
40 gfastats_data_prep n/a
41 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0
42 gfastats_plot n/a

Outputs

ID Name Description Type
Estimated Genome Size Estimated Genome Size n/a
  • File
Cutoffs for primary assembly Cutoffs for primary assembly n/a
  • File
Read Coverage and cutoffs calculation on primary assembly : Histogram plot Read Coverage and cutoffs calculation on primary assembly : Histogram plot n/a
  • File
Purged Primary Assembly Purged Primary Assembly 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 Primary Assembly (gfa) Purged Primary Assembly (gfa) n/a
  • File
Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot n/a
  • File
Cutoffs for alternate assembly Cutoffs for alternate assembly n/a
  • File
Purged Alternate assembly Purged Alternate assembly n/a
  • File
Merqury on Phased assemblies: stats Merqury on Phased assemblies: stats n/a
  • File
Merqury on Phased assemblies: Images Merqury on Phased assemblies: Images n/a
  • File
Purged Alternate assembly (gfa) Purged Alternate assembly (gfa) n/a
  • File
Assembly stats on Primary and alternate assemblies Assembly stats on Primary and alternate assemblies n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot n/a
  • File

Version History

v0.4 (latest) Created 7th Oct 2024 at 16:34 by WorkflowHub Bot

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Frozen v0.4 f4387f3

v0.3.8 Created 30th Apr 2024 at 03:02 by WorkflowHub Bot

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v0.3.7 Created 23rd Apr 2024 at 03:01 by WorkflowHub Bot

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v0.3.6 Created 27th Mar 2024 at 03:02 by WorkflowHub Bot

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v0.3.5 Created 7th Mar 2024 at 03:02 by WorkflowHub Bot

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v0.3.3 Created 24th Nov 2023 at 03:02 by WorkflowHub Bot

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v0.1 (earliest) Created 31st Oct 2023 at 03:02 by WorkflowHub Bot

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Frozen v0.1 234270a
help Creators and Submitter
Creators
Not specified
Additional credit

Galaxy, VGP

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

Views: 6648   Downloads: 1690   Runs: 1

Created: 31st Oct 2023 at 03:02

Last updated: 17th Aug 2024 at 03:02

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