Workflow Type: Galaxy
Frozen
Stable
The workflow takes a trimmed HiFi reads collection, and max coverage depth (calculated from WF1) to run Hifiasm in HiFi solo mode. It produces a Pri/Alt assembly, and runs all the QC analysis (gfastats, BUSCO, and Merqury).
Inputs
ID | Name | Description | Type |
---|---|---|---|
Estimated genome size | #main/Estimated genome size | n/a |
|
Hifiasm level of dups purging | #main/Hifiasm level of dups purging | 0 to disable, 1 to only purge contained haplotigs, 2 to purge all types of haplotigs, 3 to purge all types of haplotigs in the most aggressive way. In default, 3 for non-trio assembly, 0 for trio-binning assembly. For trio-binning assembly, only level 0 and level 1 are allowed. |
|
Meryl Database | #main/Meryl Database | n/a |
|
Trimmed HiFi Reads Collection | #main/Trimmed HiFi Reads Collection | Collection of Long reads in fastq format. |
|
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 |
---|---|---|
6 | Parse parameter value | param_value_from_file |
7 | Parse parameter value | param_value_from_file |
8 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0 |
9 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
10 | Bandage Pri | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
11 | gfastats pri | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.5+galaxy0 |
12 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
13 | Bandage alt | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
14 | gfastats alt | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
15 | BUSCO pri | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
16 | BUSCO alt | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
17 | Merqury pri/alt | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
_anonymous_output_10 | #main/_anonymous_output_10 | n/a |
|
_anonymous_output_11 | #main/_anonymous_output_11 | n/a |
|
_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
_anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
_anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
_anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
_anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
_anonymous_output_8 | #main/_anonymous_output_8 | n/a |
|
_anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
Version 1 (earliest) Created 24th Sep 2024 at 22:29 by Diego De Panis
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Version-1
67e8dc7
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ERGA
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Views: 192 Downloads: 22 Runs: 25
Created: 24th Sep 2024 at 22:29
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