Workflow Type: Galaxy
Open
Frozen
Stable
The workflow takes a Long Reads collection, Pri/Alt contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Pri and Alt contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).
Inputs
ID | Name | Description | Type |
---|---|---|---|
(Trimmed) Long Reads | (Trimmed) Long Reads | Collection of Long reads in fastq format |
|
Alt Contigs GFA | Alt Contigs GFA | Alternate contigs in GFA format from the Hifiasm run results: alt_contigs_gfa |
|
Estimated genome size | Estimated genome size | Select the est_genome_size result obtained during profiling |
|
Meryl database | Meryl database | Select the meryl_db result obtained during profiling |
|
Pri Contigs GFA | Pri Contigs GFA | Primary contigs in GFA format from the Hifiasm run results: pri_contigs_gfa |
|
Transition parameter | Transition parameter | Select the transition_param result obtained during profiling |
|
What type of Long Reads? | What type of Long Reads? | Select map-hifi if the long reads are PacBio HiFi (default), map-ont if the long reads are ONT |
|
lineage | lineage | lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ... |
|
max depth | max depth | Select the max_depth result obtained during profiling |
|
Steps
ID | Name | Description |
---|---|---|
9 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
10 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
11 | Parse parameter value | param_value_from_file |
12 | Parse parameter value | param_value_from_file |
13 | Parse parameter value | param_value_from_file |
14 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
15 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
16 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
17 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
18 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
19 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
20 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
21 | Concatenate datasets | cat1 |
22 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
23 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
24 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
25 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
26 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
27 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
28 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
29 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
30 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
31 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
32 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
33 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
Version History
Version 2 (latest) Created 1st Jun 2025 at 12:24 by Diego De Panis
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Version 1 (earliest) Created 24th Sep 2024 at 22:44 by Diego De Panis
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Created: 24th Sep 2024 at 22:44
Last updated: 1st Jun 2025 at 12:25
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