add delivery

config/config.yaml

@@ -2,6 +2,7 @@ run:
   harmonization: True
   annotation: True
   summarize: True
+  delivery: True
   tiledb: False
   ldscore: False
   metal: False
@@ -11,7 +12,7 @@ run:
 
 # paths
 sumstats_path: config/seqid_from_literature.tsv
-#dest_path: "/path/to/final/destination"
+dest_path: "/exchange/healthds/destination"
 workspace_path: "results"
 
 sumstat:

workflow/Snakefile

@@ -16,6 +16,11 @@ include: "rules/annotation.smk"
 include: "rules/summarize.smk"
 
 
+if config.get("run").get("delivery"):
+
+    include: "rules/delivery.smk"
+
+
 if config.get("run").get("metal"):
 
     include: "rules/metal.smk"

workflow/rules/common.smk

@@ -53,6 +53,10 @@ def get_final_output():
         final_output.append(ws_path("min_pvalue_table.tsv")),
         final_output.append(ws_path("inflation_factors_table.tsv"))
 
+    if config.get("run").get("delivery"):
+        final_output.append(dst_path("min_pvalue_table.tsv")),
+        final_output.append(dst_path("inflation_factors_table.tsv"))
+
     if config.get("run").get("annotation"):
         final_output.extend(
             expand(

workflow/rules/delivery.smk

@@ -0,0 +1,13 @@
+rule move_to_destination:
+    input:
+        table_minp=ws_path("min_pvalue_table.tsv"),
+        table_if=ws_path("inflation_factors_table.tsv"),
+    output:
+        table_minp=dst_path("min_pvalue_table.tsv"),
+        table_if=dst_path("inflation_factors_table.tsv"),
+    resources:
+        runtime=lambda wc, attempt: attempt * 120,
+    shell:
+        """
+        rsync -rlptoDvz {input.table_minp} {output.table_minp} && \
+        rsync -rlptoDvz {input.table_if} {output.table_if}"""