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)

Inputs

ID Name Description Type
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 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 Name of the second assembly.
  • string?
Name of primary assembly Name of primary assembly Name of the first assembly.
  • 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 Do not use.
  • File?

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_column1/2.1
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/5.8.0+galaxy0
27 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
28 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
29 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
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/1.3.9+galaxy1
39 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1
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/1.3.9+galaxy1
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+galaxy2
53 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1

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: 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 Primary Assembly (gfa) Purged Primary Assembly (gfa) n/a
  • File
Cutoffs for alternate assembly Cutoffs for alternate assembly 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
Purged Alternate assembly Purged Alternate 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
Purged Alternate assembly (gfa) Purged Alternate assembly (gfa) 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
Size Plot Size Plot n/a
  • File
Nx Plot Nx Plot n/a
  • File
Assembly statistics for purged assemblies Assembly statistics for purged assemblies n/a
  • File
clean_stats clean_stats n/a
  • File

Version History

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

Updated to v0.5


Frozen v0.5 e2bdaa2

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

Updated to v0.4


Frozen v0.4 f4387f3

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

Updated to v0.3.8


Frozen v0.3.8 511145a

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

Updated to v0.3.7


Frozen v0.3.7 559306c

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

Updated to v0.3.6


Frozen v0.3.6 d06b97d

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

Updated to v0.3.5


Frozen v0.3.5 cf9004e

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

Updated to v0.3.4


Frozen v0.3.4 dffb179

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

Updated to v0.3.3


Frozen v0.3.3 ca65f2a

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

Updated to v0.3.2


Frozen v0.3.2 f7c63a5

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

Updated to v0.3.1


Frozen v0.3.1 663620f

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

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Frozen v0.3.0 ea710ce

v0.2.0 Created 8th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.2.0


Frozen v0.2.0 a7d4e13

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

Updated to v0.1.1


Frozen v0.1.1 0981071

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

Updated to v0.1


Frozen v0.1 234270a
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Views: 8211   Downloads: 2168   Runs: 1

Created: 31st Oct 2023 at 03:02

Last updated: 5th Feb 2025 at 03:01

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