VGP assembly: training workflow

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy Europe
• Galaxy France
• Galaxy Main
• Import to another server (≥23.0+ only!)

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;

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

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:

Version History

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