Workflows

These workflows are associated with Identifying tuberculosis transmission links: from SNPs to transmission clusters

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.

flowchart TD
  0["ℹ️ Input Collection\nMTB single-end BAMs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nMTB paired-end BAMs"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Merge collections"];
  0 -->|output| 2;
  1 -->|output| 2;
  3["Samtools view BAM > SAM"];
  2 -->|output| 3;
  aa220027-9d10-4328-b2c2-e4d139d5d5bd["Output\nSamtools view on input dataset(s): filtered alignments"];
  3 --> aa220027-9d10-4328-b2c2-e4d139d5d5bd;
  style aa220027-9d10-4328-b2c2-e4d139d5d5bd stroke:#2c3143,stroke-width:4px;
  4["Sed MTB_anc to Chromosome"];
  3 -->|outputsam| 4;
  5["Samtools view SAM > BAM"];
  4 -->|output| 5;
  6["TB-profiler"];
  5 -->|outputsam| 6;
  7["Get drug resistance profile"];
  6 -->|output_txt| 7;
  8["Add Sample Name"];
  7 -->|output| 8;
  9["Concatenate DR profiles in a single table"];
  8 -->|output| 9;
  10["Cleanup the table"];
  9 -->|out_file1| 10;
	

flowchart TD
  0["ℹ️ Input Collection\nSingle-End FASTQs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nPaired-End FASTQs"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nMycobacterium_tuberculosis_ancestral_reference.gbk"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Trimmomatic"];
  0 -->|output| 3;
  4["Trimmomatic"];
  1 -->|output| 4;
  5["Mapping and variant calling of SINGLE END FASTQs with snippy"];
  3 -->|fastq_out| 5;
  2 -->|output| 5;
  6["Mapping and variant calling of PAIRED END FASTQs with snippy"];
  4 -->|fastq_out_paired| 6;
  2 -->|output| 6;
  7["Merge PE/SE VCFs in a single collection with all samples"];
  5 -->|snpvcf| 7;
  6 -->|snpvcf| 7;
  8["Merge PE/SE BAMs in a single collection with all samples Part the workflow ”Identifying DR with TB-profiler"];
  5 -->|snpsbam| 8;
  6 -->|snpsbam| 8;
  9["TB Variant Filter"];
  7 -->|output| 9;
	

flowchart TD
  0["ℹ️ Input Collection\nCollection of VCFs to analyze"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference genome of the MTBC ancestor"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Filter TB variants"];
  0 -->|output| 2;
  3["Generate the complete genome of each of the samples"];
  2 -->|output1| 3;
  1 -->|output| 3;
  ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a["Output\n#{input_file}"];
  3 --> ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a;
  style ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a stroke:#2c3143,stroke-width:4px;
  4["Concatenate genomes to build a MSA"];
  3 -->|output_file| 4;
  5["Keep only variable positions"];
  4 -->|out_file1| 5;
  6["Calculate SNP distances"];
  5 -->|output_fasta| 6;
	

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: