VGP assembly: training workflow

assembly-vgp_genome_assembly/main-workflow

Author(s)

version Version
4
last_modification Last updated
Mar 29, 2022
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
assembly

Features

Tutorial
hands_on Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00021
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nBionano_dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nHi-C_dataset_R"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nHi-C_dataset_F"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Collection\nInput Dataset Collection"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["GFA to FASTA"];
  5["GFA to FASTA"];
  6["Cutadapt"];
  3 -->|output| 6;
  7["Busco"];
  4 -->|out_fa| 7;
  8["Busco"];
  5 -->|out_fa| 8;
  9["Purge overlaps"];
  5 -->|out_fa| 9;
  10["Collapse Collection"];
  6 -->|out1| 10;
  11["Meryl"];
  6 -->|out1| 11;
  12["Map with minimap2"];
  6 -->|out1| 12;
  5 -->|out_fa| 12;
  13["Quast"];
  5 -->|out_fa| 13;
  4 -->|out_fa| 13;
  6 -->|out1| 13;
  14["Map with minimap2"];
  9 -->|split_fasta| 14;
  9 -->|split_fasta| 14;
  15["Meryl"];
  11 -->|read_db| 15;
  16["Purge overlaps"];
  12 -->|alignment_output| 16;
  17["Meryl"];
  15 -->|read_db| 17;
  18["Merqury"];
  5 -->|out_fa| 18;
  4 -->|out_fa| 18;
  15 -->|read_db| 18;
  19["Purge overlaps"];
  16 -->|pbcstat_cov| 19;
  16 -->|calcuts_cutoff| 19;
  14 -->|alignment_output| 19;
  20["GenomeScope"];
  17 -->|read_db_hist| 20;
  21["Purge overlaps"];
  19 -->|purge_dups_bed| 21;
  5 -->|out_fa| 21;
  22["Replace"];
  20 -->|summary| 22;
  23["Compute"];
  20 -->|model_params| 23;
  24["Bionano Hybrid Scaffold"];
  0 -->|output| 24;
  21 -->|get_seqs_purged| 24;
  25["Concatenate datasets"];
  21 -->|get_seqs_hap| 25;
  4 -->|out_fa| 25;
  26["Busco"];
  21 -->|get_seqs_purged| 26;
  27["Replace"];
  22 -->|outfile| 27;
  28["Compute"];
  23 -->|out_file1| 28;
  29["Concatenate datasets"];
  24 -->|ngs_contigs_scaffold_trimmed| 29;
  24 -->|ngs_contigs_not_scaffolded_trimmed| 29;
  30["Purge overlaps"];
  25 -->|out_file1| 30;
  31["Map with minimap2"];
  10 -->|output| 31;
  25 -->|out_file1| 31;
  32["Search in textfiles"];
  27 -->|outfile| 32;
  33["Advanced Cut"];
  28 -->|out_file1| 33;
  34["Advanced Cut"];
  28 -->|out_file1| 34;
  35["BWA-MEM2"];
  1 -->|output| 35;
  29 -->|out_file1| 35;
  36["BWA-MEM2"];
  2 -->|output| 36;
  29 -->|out_file1| 36;
  37["Replace"];
  29 -->|out_file1| 37;
  38["Quast"];
  29 -->|out_file1| 38;
  10 -->|output| 38;
  39["Busco"];
  29 -->|out_file1| 39;
  40["Map with minimap2"];
  30 -->|split_fasta| 40;
  30 -->|split_fasta| 40;
  41["Purge overlaps"];
  31 -->|alignment_output| 41;
  42["Convert"];
  32 -->|output| 42;
  43["Filter and merge"];
  36 -->|bam_output| 43;
  35 -->|bam_output| 43;
  44["Purge overlaps"];
  41 -->|pbcstat_cov| 44;
  41 -->|calcuts_cutoff| 44;
  40 -->|alignment_output| 44;
  45["Advanced Cut"];
  42 -->|out_file1| 45;
  46["bedtools BAM to BED"];
  43 -->|outfile| 46;
  47["PretextMap"];
  43 -->|outfile| 47;
  48["Purge overlaps"];
  44 -->|purge_dups_bed| 48;
  25 -->|out_file1| 48;
  49["Sort"];
  46 -->|output| 49;
  50["Pretext Snapshot"];
  47 -->|pretext_map_out| 50;
  51["Busco"];
  48 -->|get_seqs_purged| 51;
  52["Quast"];
  21 -->|get_seqs_purged| 52;
  48 -->|get_seqs_purged| 52;
  10 -->|output| 52;
  53["SALSA"];
  49 -->|out_file1| 53;
  37 -->|outfile| 53;
  54["BWA-MEM2"];
  1 -->|output| 54;
  53 -->|scaffolds_fasta| 54;
  55["BWA-MEM2"];
  2 -->|output| 55;
  53 -->|scaffolds_fasta| 55;
  56["Busco"];
  53 -->|scaffolds_fasta| 56;
  57["Quast"];
  53 -->|scaffolds_fasta| 57;
  10 -->|output| 57;
  58["Filter and merge"];
  55 -->|bam_output| 58;
  54 -->|bam_output| 58;
  59["PretextMap"];
  58 -->|outfile| 59;
  60["Pretext Snapshot"];
  59 -->|pretext_map_out| 60;

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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • 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”
  • 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