Scaffolding-HiC-VGP8/main

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Workflow Type: Galaxy

Scaffolding using HiC data with YAHS.

SEEK ID: https://workflowhub.eu/workflows/625?version=12

Inputs

ID Name Description Type
Database for Busco Lineage Database for Busco Lineage n/a
  • string
Estimated genome size - Parameter File Estimated genome size - Parameter File Estimated genome size from contiging workflow
  • File
Haplotype Haplotype n/a
  • string
HiC Forward reads HiC Forward reads Forward reads as a single dataset in fastq format
  • File
HiC reverse reads HiC reverse reads Reverse reads as a single dataset in fastq format
  • File
Input GFA Input GFA The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA->GFA conversion using gfastats to ensure this.
  • File
Lineage Lineage Taxonomic lineage for the organism being assembled for Busco analysis
  • string
Restriction enzymes Restriction enzymes Restriction enzymes used in preparation of Hi-C libraries.
  • string
SAK input file SAK input file n/a
  • File?
Sequence graph Sequence graph n/a
  • File?

Steps

ID Name Description
10 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
11 Parse parameter value param_value_from_file
12 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
13 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
14 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
15 Filter and merge toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
16 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
17 YAHS toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2
18 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2
19 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
20 Extract dataset __EXTRACT_DATASET__
21 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
22 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
23 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
24 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
25 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
26 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
27 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
28 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
29 gfastats_data_prep n/a
30 Filter and merge toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
31 Cut Cut1
32 Cut Cut1
33 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
34 bedtools BAM to BED toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0
35 Nx Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
36 Size Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
37 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2
38 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1
39 Extract dataset __EXTRACT_DATASET__

Outputs

ID Name Description Type
YAHS on input dataset(s): Final scaffolds agp output YAHS on input dataset(s): Final scaffolds agp output n/a
  • File
Pretext Map Before HiC scaffolding Pretext Map Before HiC scaffolding n/a
  • File
Reconciliated Scaffolds: gfa Reconciliated Scaffolds: gfa n/a
  • File
Reconciliated Scaffolds: fasta Reconciliated Scaffolds: fasta n/a
  • File
Assembly Statistics for s2 Assembly Statistics for s2 n/a
  • File
Scaffold sizes for s2 Scaffold sizes for s2 n/a
  • File
Busco Summary Busco Summary n/a
  • File
Busco Summary image Busco Summary image n/a
  • File
clean_stats clean_stats n/a
  • File
Nx Plot Nx Plot n/a
  • File
Size Plot Size Plot n/a
  • File
Pretext Map After HiC scaffolding Pretext Map After HiC scaffolding n/a
  • File

Version History

v0.2.8 (latest) Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

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Frozen v0.2.8 53e128f

v0.2.7 Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

Updated to v0.2.7


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v0.2.6 Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

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v0.2.5 Created 1st Aug 2024 at 03:01 by WorkflowHub Bot

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v0.2.4 Created 30th May 2024 at 11:35 by WorkflowHub Bot

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v0.2.3 Created 24th Apr 2024 at 03:01 by WorkflowHub Bot

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Frozen v0.2.3 7479a72

v0.2.2 Created 27th Mar 2024 at 03:02 by WorkflowHub Bot

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Frozen v0.2.2 8b8fe66

v0.2.1 Created 24th Nov 2023 at 03:02 by WorkflowHub Bot

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Frozen v0.2.1 faa9803

v0.2 Created 17th Nov 2023 at 03:02 by WorkflowHub Bot

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Frozen v0.2 b9afa62

v0.1.2 Created 16th Nov 2023 at 03:02 by WorkflowHub Bot

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Frozen v0.1.2 81d58fc

v0.1.1 Created 31st Oct 2023 at 03:02 by WorkflowHub Bot

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Frozen v0.1.1 bde67a2

v0.1 (earliest) Created 27th Oct 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 95a269d
help Creators and Submitter
Creators
Not specified
Additional credit

VGP, Galaxy

Submitter
Tools
gfastats
Bwa-mem2
BUSCO
BEDTools
ggplot2
License
Creative Commons Attribution 4.0 International
Activity

Views: 5552   Downloads: 1385   Runs: 0

Created: 27th Oct 2023 at 03:01

Last updated: 7th Oct 2024 at 16:33

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