Workflows

These workflows are associated with Proteogenomics 1: Database Creation

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.

GTN Proteogenomics1 Database Creation

Last updated Feb 8, 2021

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

flowchart TD
  0["Input dataset"];
  1["Input dataset"];
  2["Input dataset"];
  3["HISAT2"];
  0 -->|output| 3;
  4["Replace Text"];
  1 -->|output| 4;
  5["FASTA-to-Tabular"];
  2 -->|output| 5;
  6["FreeBayes"];
  3 -->|output_alignments| 6;
  7["StringTie"];
  4 -->|outfile| 7;
  3 -->|output_alignments| 7;
  8["Filter Tabular"];
  5 -->|output| 8;
  9["CustomProDB"];
  3 -->|output_alignments| 9;
  6 -->|output_vcf| 9;
  10["GffCompare"];
  4 -->|outfile| 10;
  7 -->|output_gtf| 10;
  11["SQLite to tabular"];
  9 -->|output_genomic_mapping_sqlite| 11;
  12["SQLite to tabular"];
  9 -->|output_variant_annotation_sqlite| 12;
  13["FASTA Merge Files and Filter Unique Sequences"];
  9 -->|output_rpkm| 13;
  9 -->|output_snv| 13;
  9 -->|output_indel| 13;
  14["FASTA-to-Tabular"];
  9 -->|output_rpkm| 14;
  15["Convert gffCompare annotated GTF to BED"];
  10 -->|transcripts_annotated| 15;
  16["Column Regex Find And Replace"];
  11 -->|query_results| 16;
  17["Column Regex Find And Replace"];
  12 -->|query_results| 17;
  18["FASTA-to-Tabular"];
  13 -->|output| 18;
  19["Filter Tabular"];
  14 -->|output| 19;
  20["Translate BED transcripts"];
  15 -->|output| 20;
  21["Query Tabular"];
  17 -->|out_file1| 21;
  22["Column Regex Find And Replace"];
  18 -->|output| 22;
  23["Concatenate datasets"];
  19 -->|output| 23;
  8 -->|output| 23;
  24["bed to protein map"];
  20 -->|translation_bed| 24;
  25["Tabular-to-FASTA"];
  22 -->|out_file1| 25;
  26["Concatenate datasets"];
  24 -->|output| 26;
  16 -->|out_file1| 26;
  27["FASTA Merge Files and Filter Unique Sequences"];
  2 -->|output| 27;
  25 -->|output| 27;
  20 -->|translation_fasta| 27;
  28["Query Tabular"];
  26 -->|out_file1| 28;

	

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: