Change test to only run with --dry-run

Author: fcaretti

Diff for: .github/workflows/main.yml

@@ -42,9 +42,9 @@ jobs:
     - name: Test workflow
       uses: snakemake/[email protected]
       with:
-        directory: .
+        directory: .test
         snakefile: workflow/Snakefile
-        args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
+        args: "--dry-run --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
 
     - name: Test report
       uses: snakemake/[email protected]

Diff for: .test/config.yml

@@ -0,0 +1,6 @@
+data:
+  folder: ".test/data"
+
+reference:
+  folder: ".test/data"
+  genome: "placeholder.fa"

Diff for: .test/data/placeholder.bam

@@ -1,10 +1,11 @@
-# Snakemake workflow: `<name>`
+# Snakemake workflow: SNPs from RNA
 
 [![Snakemake](https://img.shields.io/badge/snakemake-≥6.3.0-brightgreen.svg)](https://snakemake.github.io)
 [![GitHub actions status](https://github.com/<owner>/<repo>/workflows/Tests/badge.svg?branch=main)](https://github.com/<owner>/<repo>/actions?query=branch%3Amain+workflow%3ATests)
 
 
-A Snakemake workflow for `<description>`
+A Snakemake workflow for the call of Single Nucleotide Polymorphisms (SNPs) from RNA-seq data.
+The workflow starts from aligned .bam files and outputs variants called by FreeBayes (or GATK's HaplotypeCaller) and annotated by VEP.
 
 
 ## Usage
@@ -13,9 +14,3 @@ The usage of this workflow is described in the [Snakemake Workflow Catalog](http
 
 If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) <repo>sitory and its DOI (see above).
 
-# TODO
-
-* Replace `<owner>` and `<repo>` everywhere in the template (also under .github/workflows) with the correct `<repo>` name and owning user or organization.
-* Replace `<name>` with the workflow name (can be the same as `<repo>`).
-* Replace `<description>` with a description of what the workflow does.
-* The workflow will occur in the snakemake-workflow-catalog once it has been made public. Then the link under "Usage" will point to the usage instructions if `<owner>` and `<repo>` were correctly set.