ERGA HiC Pri Scaffolding+QC YaHS v2409 (WF4)
Version 1

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Workflow Type: Galaxy
Stable

The workflow takes trimmed HiC forward and reverse reads, and Pri/Alt assemblies to produce a scaffolded primary assembliy (and alternate contigs) using YaHS. It also runs all the QC analyses (gfastats, BUSCO, and Merqury).

SEEK ID: https://workflowhub.eu/workflows/1164?version=1

Inputs

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

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 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
10 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
11 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
12 Filter and merge toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
13 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
14 YAHS toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2
15 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2
16 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
17 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
18 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
19 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0
20 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
21 Filter and merge toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
22 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
23 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File

Version History

Version 1 (earliest) Created 24th Sep 2024 at 22:54 by Diego De Panis

Initial commit


Frozen Version-1 8a34969
help Creators and Submitter
Creator
Additional credit

ERGA

Submitter
Discussion Channel
https://github.com/ERGA-consortium/pipelines/discussions
Tools
Bwa-mem2
gfastats
BUSCO
Merqury
License
MIT License
Activity

Views: 876   Downloads: 84   Runs: 37

Created: 24th Sep 2024 at 22:54

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Total size: 214 KB
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