diff --git a/docs/installation.md b/docs/installation.md index 43fc0647..9b8f6e0b 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -139,11 +139,15 @@ Given that the workflow has been properly deployed and configured, run Snakemake Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment. -This workflow is written with Snakemake and details and tools are described in the -[Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog?usage=IKIM-Essen/uncovar). +If the user is only interested in getting a specific result, every intermediate + file of the analysis can be generated with including it in the execution + prompt, e.g. the FDR-controlled variant callings with major impact: -If you use this workflow in your work, don't forget to give credits to the -authors by citing the URL of this repository and its DOI (see above). +```sh + snakemake --cores all --use-conda results/{date}/filtered-calls/ref~main/{sample}.subclonal-major.nofilter.orf.bcf +``` + +exchanging `date` and `sample` accordingly. ---------------- ## General settings @@ -159,3 +163,9 @@ The incoming directory should contain paired end reads in (compressed) FASTQ format. UnCoVar automatically copies your data into the data directory and moves all files from incoming directory to the archive. After the analysis, all results are compressed and saved alongside the reads. + +This workflow is written with Snakemake. Details are described in the +[Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog?usage=IKIM-Essen/uncovar). + +If you use this workflow in your work, don't forget to give credits to the +authors by citing the URL of this repository and its DOI (see above). diff --git a/mkdocs.yml b/mkdocs.yml index 3467c546..119e770b 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -8,7 +8,7 @@ repo_name: "" nav: - Overview: index.md - - Installation: installation.md + - Installation + Execution: installation.md - The Report: user-guide.md - Advanced Configuration: configuration.md - Tools: tools.md