Snakefile moved to workflow directory

Author: AntonieV

.github/workflows/main.yaml

@@ -17,7 +17,7 @@ jobs:
         uses: snakemake/[email protected]
         with:
           directory: .test
-          snakefile: Snakefile
+          snakefile: workflow/Snakefile
           args: "--lint"
 
   Testing:
@@ -32,12 +32,12 @@ jobs:
       uses: snakemake/[email protected]
       with:
         directory: .test
-        snakefile: Snakefile
+        snakefile: workflow/Snakefile
         args: "--use-conda --show-failed-logs --cores 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
 
     - name: Test report
       uses: snakemake/[email protected]
       with:
         directory: .test
-        snakefile: Snakefile
+        snakefile: workflow/Snakefile
         args: "--report report.zip"

Snakefile workflow/Snakefile

@@ -30,11 +30,11 @@
 #        * add header to results of BLAST analysis (rule blast_header) and create plots (rule plots_blast)
 
 
-include: "workflow/rules/common.smk"
-include: "workflow/rules/qc.smk"
-include: "workflow/rules/cutadapt.smk"
-include: "workflow/rules/noderad.smk"
-include: "workflow/rules/evaluation.smk"
+include: "rules/common.smk"
+include: "rules/qc.smk"
+include: "rules/cutadapt.smk"
+include: "rules/noderad.smk"
+include: "rules/evaluation.smk"
 
 rule all:
     input: all_input