ERGA HiC Collapsed Scaffolding+QC YaHS v2311 (WF4)
Version 1

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Workflow Type: Galaxy
Work-in-progress

The workflow takes trimmed HiC forward and reverse reads, and one assembly (e.g.: Hap1 or Pri or Collapsed) to produce a scaffolded assembly using YaHS. It also runs all the QC analyses (gfastats, BUSCO, and Merqury).

SEEK ID: https://workflowhub.eu/workflows/702?version=1

Inputs

ID Name Description Type
Estimated genome size Estimated genome size n/a
  • File
HiC F trimmed HiC F trimmed HiC forward reads (already trimmed)
  • File
HiC R trimmed HiC R trimmed HiC reverse reads (already trimmed)
  • File
Meryl database Meryl database n/a
  • File
Purged GFA Purged GFA gfa assembly file to scaffold
  • File
lineage lineage lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ...
  • string

Steps

ID Name Description
6 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
7 Parse parameter value param_value_from_file
8 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
9 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
10 Filter and merge toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
11 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0
12 YAHS toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1
13 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1
14 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
15 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
16 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
17 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
18 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
19 Filter and merge toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
20 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0
21 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1

Outputs

ID Name Description Type
_anonymous_output_1 _anonymous_output_1 n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File

Version History

Version 1 (earliest) Created 9th Jan 2024 at 11:00 by Diego De Panis

Initial commit


Open master f664a12
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Additional credit

ERGA

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Discussion Channel
https://github.com/ERGA-consortium/pipelines/discussions
License
MIT License
Activity

Views: 2516   Downloads: 213   Runs: 0

Created: 9th Jan 2024 at 11:00

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