https://github.com/baerlachlan/smk-rnaseq-gatk-variants
Snakemake implementation of the GATK best-practices workflow for RNA-seq short variant discovery
Science Score: 13.0%
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Low similarity (9.0%) to scientific vocabulary
Repository
Snakemake implementation of the GATK best-practices workflow for RNA-seq short variant discovery
Basic Info
Statistics
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 4
Metadata Files
README.md
Snakemake workflow for variant calling from RNA-seq data
This Snakemake workflow implements the GATK best-practices workflow for RNA-seq short variant discovery.
Standardised usage
Standardised usage of this workflow is described in the Snakemake Workflow Catalog.
However, Snakemake standardised usage requires internet access which is commonly unavailable in an HPC environment. If the intention is to run the workflow in an offline environment, please see Recommended usage.
Recommended usage
For compatibility across environments, the source code of this workflow is available via Releases.
- Download and extract the workflow's latest release
- Remove unrequired files
bash rm .gitignore .snakemake-workflow-catalog.yml - Follow the instructions in
config/README.mdto modifyconfig/samples.tsvandconfig/units.tsv - Follow the comments in
config/config.yamlto configure the workflow parameters - Use the example profile in
workflow/profiles/example/config.v8+.yamlas a guide to fine-tune workflow-specific resource configuration- NOTE: the example profile has been designed for compatibility with my SLURM profile
- To automatically enable a workflow-specific profile, move it to
workflow/profiles/default, for example:bash cp -r workflow/profiles/example workflow/profiles/default
- Execute the workflow
bash snakemake
Testing
Example data and configurations are available for testing of this workflow.
Backup the example configuration, and copy the test configuration in its place:
```bash
Backup example config
mv config/ config_example/
Test paired-end
cp -r .test/config_pe/ config/
Or test single-end
cp -r .test/config_se/ config/ ```
The example data is small, so the test workflow profile can be used upon execution.
To keep intermediate files, specify the --notemp flag.
bash
snakemake --notemp --workflow-profile workflow/profiles/test
Owner
- Name: Lachlan Baer
- Login: baerlachlan
- Kind: user
- Location: Adelaide, South Australia
- Company: University of Adelaide
- Twitter: baerlachlan
- Repositories: 9
- Profile: https://github.com/baerlachlan