feat(snakemake): produce DAG of run

Add step to pipeline to produce a DAG of the pipeline. As a workflow manager is already in use (Snakemake), there is no reason not to make it self documenting.
IMS-Bio2Core-Facility · Jun 11, 2021 · 27d420c · 27d420c
1 parent 5c34730
commit 27d420c
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diff --git a/Snakefile b/Snakefile
@@ -9,8 +9,19 @@ RESULTS = config["results_dir"]
 
 rule all:
         input:
+                RESULTS + "dag.png",
                 RESULTS + "process/sorted_isoforms.xlsx",
 
+rule dag:
+        output:
+                dag = RESULTS + "dag.png",
+        conda:
+                ENVS + "dag.yml"
+        shell:
+                "snakemake -np --dag &> /dev/null | "
+                "dot -Tpng "
+                "> {output.dag}"
+
 rule ids:
         params:
                 url = config["gencode_url"],

diff --git a/environments/dag.yml b/environments/dag.yml
@@ -0,0 +1,7 @@
+name: mane
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - snakemake==6.4.0