Purge-duplicate-contigs-VGP6/main
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Workflow Type: Galaxy
Frozen
Frozen
Purge contigs marked as duplicates by purge_dups.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Assembly Name | Assembly Name | For workflow report. |
|
| Database for Busco Lineage | Database for Busco Lineage | Database to use for Busco Lineages. |
|
| Estimated genome size - Parameter File | Estimated genome size - Parameter File | Estimated genome size generated by contiging workflows. |
|
| Genomescope model parameters | Genomescope model parameters | GenomeScope model parameters generated by K-mer profiling workflow. |
|
| Hifiasm Alternate assembly | Hifiasm Alternate assembly | Alternate assembly generated by contiging workflow in fasta format. |
|
| Hifiasm Primary assembly | Hifiasm Primary assembly | Primary assembly generated by contiging workflow in fasta format. |
|
| Lineage | Lineage | Taxonomic lineage for the organism being assembled for Busco analysis. |
|
| Meryl Database | Meryl Database | Meryl database generated by K-mer profiling workflow. |
|
| Name of alternate assembly | Name of alternate assembly | Name of the second assembly. |
|
| Name of primary assembly | Name of primary assembly | Name of the first assembly. |
|
| 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. |
|
| Species Name | Species Name | For workflow report. |
|
| What sequences are you purging? | What sequences are you purging? | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 13 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 14 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 15 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2 |
| 16 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy1 |
| 17 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 18 | Estimated genome size | param_value_from_file |
| 19 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 20 | Awk command for primary assembly | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 21 | Map parameter value | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 22 | Awk command for alternate assembly 2 | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 23 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2 |
| 24 | Cut | Cut1 |
| 25 | Cut | Cut1 |
| 26 | Parse parameter value | param_value_from_file |
| 27 | Parse parameter value | param_value_from_file |
| 28 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy1 |
| 29 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy1 |
| 30 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy1 |
| 31 | Concatenate multiple datasets or collections | cat1 |
| 32 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 33 | Compleasm on purged primary/hap1 assembly | toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3 |
| 34 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 35 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 36 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2 |
| 37 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy1 |
| 38 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 39 | gfastats_data_prep | n/a |
| 40 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy1 |
| 41 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2 |
| 42 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy1 |
| 43 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy1 |
| 44 | Rename and unify fasta | n/a |
| 45 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 46 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 47 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 48 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 49 | Compleasm on purged alternate/hap2 assembly | toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3 |
| 50 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 51 | gfastats_data_prep | n/a |
| 52 | merqury_QV | __EXTRACT_DATASET__ |
| 53 | output_merqury.spectra-cn.fl | __EXTRACT_DATASET__ |
| 54 | output_merqury.spectra-asm.fl | __EXTRACT_DATASET__ |
| 55 | output_merqury.assembly_01.spectra-cn.fl | __EXTRACT_DATASET__ |
| 56 | merqury_stats | __EXTRACT_DATASET__ |
| 57 | output_merqury.assembly_02.spectra-cn.fl | __EXTRACT_DATASET__ |
| 58 | Join two Datasets | join1 |
| 59 | gfastats_plot | n/a |
| 60 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy3 |
| 61 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Species for report | Species for report | n/a |
|
| Assembly for report | Assembly for report | n/a |
|
| Estimated Genome Size | Estimated Genome Size | n/a |
|
| Lineage for report | Lineage for report | n/a |
|
| Read Coverage and cutoffs calculation on primary assembly: Histogram plot | Read Coverage and cutoffs calculation on primary assembly: Histogram plot | n/a |
|
| Cutoffs for primary assembly | Cutoffs for primary assembly | n/a |
|
| Purged Primary Assembly | Purged Primary Assembly | n/a |
|
| Purged Primary Assembly (gfa) | Purged Primary Assembly (gfa) | n/a |
|
| hap1 assembly: Full Table | Compleasm on purged primary/hap1 assembly: Full Table | n/a |
|
| hap1 assembly: Miniprot | Compleasm on purged primary/hap1 assembly: Miniprot | n/a |
|
| hap1 assembly: Full Table Busco | Compleasm on purged primary/hap1 assembly: Full Table Busco | n/a |
|
| hap1 assembly: Translated Proteins | Compleasm on purged primary/hap1 assembly: Translated Proteins | n/a |
|
| hap1 assembly: Summary | Compleasm on purged primary/hap1 assembly: Summary | n/a |
|
| Read Coverage and cutoffs calculation on alternate assembly: Histogram Plot | Read Coverage and cutoffs calculation on alternate assembly: Histogram Plot | n/a |
|
| Cutoffs for alternate assembly | Cutoffs for alternate assembly | n/a |
|
| Purged Alternate Assembly | Purged Alternate Assembly | n/a |
|
| Name mapping Alternate assembly | Name mapping Alternate assembly | n/a |
|
| Merqury on Phased assemblies: stats | Merqury on Phased assemblies: stats | n/a |
|
| Merqury on Phased assemblies: Images | Merqury on Phased assemblies: Images | n/a |
|
| Purged Alternate assembly (gfa) | Purged Alternate assembly (gfa) | n/a |
|
| hap2 assembly: Full Table Busco | Compleasm on purged alternate/hap2 assembly: Full Table Busco | n/a |
|
| hap2 assembly: Translated Proteins | Compleasm on purged alternate/hap2 assembly: Translated Proteins | n/a |
|
| hap2 assembly: Summary | Compleasm on purged alternate/hap2 assembly: Summary | n/a |
|
| hap2 assembly: Miniprot | Compleasm on purged alternate/hap2 assembly: Miniprot | n/a |
|
| hap2 assembly: Full Table | Compleasm on purged alternate/hap2 assembly: Full Table | n/a |
|
| merqury_QV | merqury_QV | n/a |
|
| output_merqury.spectra-cn.fl | output_merqury.spectra-cn.fl | n/a |
|
| output_merqury.spectra-asm.fl | output_merqury.spectra-asm.fl | n/a |
|
| output_merqury.assembly_01.spectra-cn.fl | output_merqury.assembly_01.spectra-cn.fl | n/a |
|
| merqury_stats | merqury_stats | n/a |
|
| output_merqury.assembly_02.spectra-cn.fl | output_merqury.assembly_02.spectra-cn.fl | n/a |
|
| Nx Plot | Nx Plot | n/a |
|
| Size Plot | Size Plot | n/a |
|
| Assembly statistics for purged assemblies | Assembly statistics for purged assemblies | n/a |
|
| clean_stats | clean_stats | n/a |
|
Version History
v0.10.5 (latest) Created 29th Jan 2026 at 03:01 by WorkflowHub Bot
Updated to v0.10.5
Frozen
v0.10.50ebab1d
v0.1 (earliest) Created 31st Oct 2023 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
234270a
Creators and Submitter
Activity
Views: 24159 Downloads: 57496 Runs: 4
Created: 31st Oct 2023 at 03:02
Last updated: 29th Jan 2026 at 03:01
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AttributionsNone
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