Apply suggestions from code review

Author: johanneskoester

.github/workflows/main.yml

@@ -62,7 +62,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Download reference genome
-        uses: snakemake/snakemake-github-action@fix/revive-stagein
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: "."
           snakefile: "workflow/Snakefile"
@@ -72,7 +72,7 @@ jobs:
             pip install snakemake-storage-plugin-http
 
       - name: Download truthsets
-        uses: snakemake/snakemake-github-action@fix/revive-stagein
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: "."
           snakefile: "workflow/Snakefile"
@@ -86,28 +86,28 @@ jobs:
       # because their modification dates are too new or too old.
       # (as git does not preserve modification dates)
       - name: Fix modification dates
-        uses: snakemake/snakemake-github-action@fix/revive-stagein
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: "."
           snakefile: "workflow/Snakefile"
-          args: "--cores 1 --touch resources/regions/giab-NA12878-agilent-200M/test-regions.cov-*.bed"
+          args: "--cores 1 --touch resources/regions/*/test-regions.cov-*.bed"
           stagein: |
             pip install snakemake-storage-plugin-zenodo 
             pip install snakemake-storage-plugin-http
 
       - name: Run analysis
-        uses: snakemake/snakemake-github-action@fix/revive-stagein
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: "."
           snakefile: "workflow/Snakefile"
           args: >
-            --cores 2 --use-conda --conda-cleanup-pkgs cache
+            --cores 2 --use-conda --conda-cleanup-pkgs cache --verbose
           stagein: |
             pip install snakemake-storage-plugin-zenodo 
             pip install snakemake-storage-plugin-http
 
       - name: Create report
-        uses: snakemake/snakemake-github-action@fix/revive-stagein
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: "."
           snakefile: "workflow/Snakefile"