Workflow Type: Galaxy
Open
Work-in-progress
The workflow takes a trimmed Illumina WGS paired-end reads collection, Collapsed contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Collapsed contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).
Inputs
ID | Name | Description | Type |
---|---|---|---|
Estimated genome size | #main/Estimated genome size | n/a |
|
GFA contigs | #main/GFA contigs | n/a |
|
Meryl database | #main/Meryl database | n/a |
|
ONT reads | #main/ONT reads | n/a |
|
Transition parameter | #main/Transition parameter | n/a |
|
lineage | #main/lineage | lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ... |
|
max depth | #main/max depth | n/a |
|
Steps
ID | Name | Description |
---|---|---|
7 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
8 | Parse parameter value | param_value_from_file |
9 | Parse parameter value | param_value_from_file |
10 | Parse parameter value | param_value_from_file |
11 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
12 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0 |
13 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0 |
14 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
15 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
16 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
17 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
18 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
19 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0 |
20 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
output | #main/output | n/a |
|
Version History
Version 1 (earliest) Created 9th Jan 2024 at 10:40 by Diego De Panis
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ERGA
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Views: 2296 Downloads: 196 Runs: 0
Created: 9th Jan 2024 at 10:40
Last updated: 9th Jan 2024 at 10:44
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