Workflow Type: Galaxy
Frozen
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. |
|
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. |
|
SAK input file | SAK input file | Do not use. |
|
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 |
|
Cutoffs for primary assembly | Cutoffs for primary assembly | n/a |
|
Read Coverage and cutoffs calculation on primary assembly : Histogram plot | Read Coverage and cutoffs calculation on primary assembly : Histogram plot | n/a |
|
Purged Primary Assembly | Purged Primary Assembly | n/a |
|
Busco on Purged Primary assembly: summary image | Busco on Purged Primary assembly: summary image | n/a |
|
Busco on Purged Primary assembly: short summary | Busco on Purged Primary assembly: short summary | n/a |
|
Purged Primary Assembly (gfa) | Purged Primary Assembly (gfa) | n/a |
|
Cutoffs for alternate assembly | Cutoffs for alternate assembly | n/a |
|
Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot | Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot | n/a |
|
Purged Alternate assembly | Purged Alternate assembly | n/a |
|
Merqury on Phased assemblies: Images | Merqury on Phased assemblies: Images | n/a |
|
Merqury on Phased assemblies: stats | Merqury on Phased assemblies: stats | n/a |
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Purged Alternate assembly (gfa) | Purged Alternate assembly (gfa) | 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 |
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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 |
|
Size Plot | Size Plot | n/a |
|
Nx Plot | Nx Plot | n/a |
|
Assembly statistics for purged assemblies | Assembly statistics for purged assemblies | n/a |
|
clean_stats | clean_stats | n/a |
|
Version History
v0.1 (earliest) Created 31st Oct 2023 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
234270a
Creators and Submitter
Creators
Not specifiedAdditional credit
Galaxy, VGP
Submitter
Tools
Activity
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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