Purge Duplicate Contigs

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

1. Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow)
2. Primary Assembly (hap1) [fasta] (Generated by the contigging workflow)
3. Alternate Assembly (hap2) [fasta] (Generated by the contigging workflow)
4. K-mer database [meryldb] (Generated by the k-mer profiling workflow)
5. Genomescope model parameters [txt] (Generated by the k-mer profiling workflow)
6. Estimated Genome Size [txt]
7. Database for busco lineage (recommended: latest)
8. Lineage of your species for Busco Orthologs (recommended: vertebrata)
9. Name of first haplotype
10. Name of second haplotype

Outputs

1. Haplotype 1 purged assembly (Fasta and gfa)
2. Haplotype 2 purged assembly (Fasta and gfa)
3. QC: BUSCO report for both assemblies
4. QC: Merqury report for both assemblies
5. QC: Assembly statistics for both assemblies
6. QC: Nx plot for both assemblies
7. QC: Size plot for both assemblies

Changelog

[0.4] 2024-08-13

Added

• Workflow report

Changed

• Expose Busco lineage database parameter
• Fix bug that was causing issues when merging the assembly statistics: The presence of the '#' character caused the tables to join incorrectly, and the numbers did not match the metrics

[0.3.8] 2024-04-23

Added

• Add Busco Gff output

[0.3.7] 2024-04-22

Automatic update

• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.27+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3 was updated to toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4

[0.3.6] 2024-03-25

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.27+galaxy0

[0.3.5] 2024-03-04

Automatic update

• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy0

[0.3.4] 2024-02-15

• Remove tag filtering
• Add merqury histogram outputs

[0.3.3] 2023-11-20

• Fix author in dockstore

[0.3.2] - 2023-11-15

Added

• more descriptive lables for inputs

[0.3.1] 2023-11-09

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2 was updated to toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2 was updated to toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
• toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0 was updated to toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1
• toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1

[0.3] - 2023-11-08

Added

• Made BUSCO lineage selectable from workflow launch interface

Changed

• Change BUSCO lineage input parameter name from Provide lineage for BUSCO (e.g., Vertebrata) to Lineage

[0.2.0] - 2023-11-07

Added

• Tag filtering for inputs
• Changed parameters of gfastats for postprocessing of contigs generated with purge_dups. Specfically:
  • "Terminal overlap selection" is set to "Yes"
  • "Generated the initial set of paths" is set to "No"

[0.1.1] - 2023-11-01

Added

• More explicit tags for readability

[0.1] - 2023-10-26

Added

• Workflow for purging duplication in contigs

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0
• toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
• param_value_from_file
• toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
• Cut1
• cat1
• toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
• __EXTRACT_DATASET__
• join1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1