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=13

Steps

ID Name Description
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 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
14 Estimated genome size param_value_from_file
15 Awk command for primary assembly toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
16 Awk command for alternate assembly 2 toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
17 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
18 Cut Cut1
19 Cut Cut1
20 Parse parameter value param_value_from_file
21 Parse parameter value param_value_from_file
22 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
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 Concatenate datasets cat1
26 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
27 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
28 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
29 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
30 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
31 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
32 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
33 gfastats_data_prep n/a
34 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
35 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
36 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
37 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
38 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
39 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
40 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
41 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
42 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
43 gfastats_data_prep n/a
44 merqury_QV __EXTRACT_DATASET__
45 output_merqury.spectra-cn.fl __EXTRACT_DATASET__
46 output_merqury.spectra-asm.fl __EXTRACT_DATASET__
47 output_merqury.assembly_01.spectra-cn.fl __EXTRACT_DATASET__
48 merqury_stats __EXTRACT_DATASET__
49 output_merqury.assembly_02.spectra-cn.fl __EXTRACT_DATASET__
50 Join two Datasets join1
51 gfastats_plot n/a
52 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
53 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1

Version History

v0.10 (latest) Created 16th May 2025 at 03:02 by WorkflowHub Bot

Updated to v0.10


Frozen v0.10 9e81880

v0.9 Created 15th May 2025 at 03:02 by WorkflowHub Bot

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Frozen v0.9 8c31985

v0.8 Created 26th Mar 2025 at 11:59 by WorkflowHub Bot

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v0.7 Created 26th Mar 2025 at 11:59 by WorkflowHub Bot

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Frozen v0.7 b47c2ee

v0.6 Created 15th Feb 2025 at 03:02 by WorkflowHub Bot

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Frozen v0.6 83f84da

v0.5 Created 5th Feb 2025 at 03:01 by WorkflowHub Bot

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Frozen v0.5 e2bdaa2

v0.4 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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Frozen v0.3.8 511145a

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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v0.3.4 Created 17th Feb 2024 at 03:01 by WorkflowHub Bot

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

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v0.3.2 Created 17th Nov 2023 at 03:02 by WorkflowHub Bot

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v0.3.1 Created 16th Nov 2023 at 03:01 by WorkflowHub Bot

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v0.3.0 Created 9th Nov 2023 at 03:02 by WorkflowHub Bot

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v0.1.1 Created 4th Nov 2023 at 03:02 by WorkflowHub Bot

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Frozen v0.1.1 0981071

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
compleasm
License
Creative Commons Attribution 4.0 International
Activity

Views: 11884   Downloads: 3736   Runs: 3

Created: 31st Oct 2023 at 03:02

Last updated: 16th May 2025 at 03:02

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