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.
From BAMs to drug resistance prediction with TB-profiler
Last updated Mar 16, 2022
Launch in Tutorial Modequestion
License:
None Specified, defaults to
CC-BY-4.0
Tests: ❌
Results: Not yet automated
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;
From VCFs to SNP distance matrix
Last updated Mar 16, 2022
Launch in Tutorial Modequestion
License:
None Specified, defaults to
CC-BY-4.0
Tests: ❌
Results: Not yet automated