VGP assembly: training workflow

assembly-vgp_genome_assembly/main-workflow

Author(s)

Version
4
Last updated
Mar 29, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
assembly

Features
Tutorial
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00021
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
out_fa
out_fa
out_fa
out1
out1
out1
out_fa
out_fa
out_fa
out1
split_fasta
split_fasta
read_db
alignment_output
read_db
out_fa
out_fa
read_db
pbcstat_cov
calcuts_cutoff
alignment_output
read_db_hist
purge_dups_bed
out_fa
summary
model_params
output
get_seqs_purged
get_seqs_hap
out_fa
get_seqs_purged
outfile
out_file1
ngs_contigs_scaffold_trimmed
ngs_contigs_not_scaffolded_trimmed
out_file1
output
out_file1
outfile
out_file1
out_file1
output
out_file1
output
out_file1
out_file1
out_file1
output
out_file1
split_fasta
split_fasta
alignment_output
output
bam_output
bam_output
pbcstat_cov
calcuts_cutoff
alignment_output
out_file1
outfile
outfile
purge_dups_bed
out_file1
output
pretext_map_out
get_seqs_purged
get_seqs_purged
get_seqs_purged
output
out_file1
outfile
output
scaffolds_fasta
output
scaffolds_fasta
scaffolds_fasta
scaffolds_fasta
output
bam_output
bam_output
outfile
pretext_map_out
ℹ️ Input Dataset
Bionano_dataset
ℹ️ Input Dataset
Hi-C_dataset_R
ℹ️ Input Dataset
Hi-C_dataset_F
ℹ️ Input Collection
Input Dataset Collection
GFA to FASTA
GFA to FASTA
Cutadapt
Busco
Busco
Purge overlaps
Collapse Collection
Meryl
Map with minimap2
Quast
Map with minimap2
Meryl
Purge overlaps
Meryl
Merqury
Purge overlaps
GenomeScope
Purge overlaps
Replace
Compute
Bionano Hybrid Scaffold
Concatenate datasets
Busco
Replace
Compute
Concatenate datasets
Purge overlaps
Map with minimap2
Search in textfiles
Advanced Cut
Advanced Cut
BWA-MEM2
BWA-MEM2
Replace
Quast
Busco
Map with minimap2
Purge overlaps
Convert
Filter and merge
Purge overlaps
Advanced Cut
bedtools BAM to BED
PretextMap
Purge overlaps
Sort
Pretext Snapshot
Busco
Quast
SALSA
BWA-MEM2
BWA-MEM2
Busco
Quast
Filter and merge
PretextMap
Pretext Snapshot

Inputs

Input Label
Input dataset Bionano_dataset
Input dataset Hi-C_dataset_R
Input dataset Hi-C_dataset_F
Input dataset collection Input Dataset Collection

Outputs

From Output Label

Tools

Tool Links
Convert characters1
cat1
sort1
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
8 b57efed60 2022-03-29 05:59:56 VGP training: fix duplication problem (#3271)
7 f764939f8 2022-02-16 19:36:00 Update VGP training 06.02: synthetic reads (#3157)
6 5552083dd 2022-01-25 11:07:55 Fix bug
5 f7354f457 2022-01-25 11:00:31 Fix workflow lint
4 e87377be9 2022-01-25 10:56:29 Include Linelle and update workflow
3 a45e18740 2021-06-03 21:04:48 workflow tag and annotation
2 54179df03 2021-06-03 20:47:22 update tools
1 3309edda7 2021-06-03 20:07:52 add vgp training skeleton from workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows