[dev] (bwa): Automatix prefix detection (snakemake#228)

bio/bwa-mem2/index/wrapper.py

@@ -16,7 +16,11 @@
     raise ValueError("Please provide exactly one reference genome as input.")
 
 # Prefix that should be used for the database
-prefix = snakemake.params.get("prefix", "")
+prefix = None
+if "prefix" in snakemake.params.keys():
+    prefix = snakemake.params["prefix"]
+else:
+    prefix = splitext(snakemake.output[0])[0]
 
 if len(prefix) > 0:
     prefix = "-p " + prefix

bio/bwa-mem2/mem-samblaster/wrapper.py

@@ -14,6 +14,14 @@
 sort_extra = snakemake.params.get("sort_extra", "")
 samblaster_extra = snakemake.params.get("samblaster_extra", "")
 
+index = None
+if "index" in snakemake.params.keys():
+    index = snakemake.params["index"]
+elif "index" in snakemake.input.keys():
+    index = path.splitext(snakemake.input["index"])[0]
+else:
+    raise ValueError("Could not find BWA index prefix")
+
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
 # Check inputs/arguments.
@@ -27,7 +35,7 @@
     "(bwa-mem2 mem"
     " -t {snakemake.threads}"
     " {extra}"
-    " {snakemake.params.index}"
+    " {index}"
     " {snakemake.input.reads}"
     " | samblaster"
     " {samblaster_extra}"

bio/bwa-mem2/mem/wrapper.py

@@ -18,6 +18,14 @@
 sort_order = snakemake.params.get("sort_order", "coordinate")
 sort_extra = snakemake.params.get("sort_extra", "")
 
+index = None
+if "index" in snakemake.params.keys():
+    index = snakemake.params["index"]
+elif "index" in snakemake.input.keys():
+    index = path.splitext(snakemake.input["index"])[0]
+else:
+    raise ValueError("Could not find BWA index prefix")
+
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
 # Check inputs/arguments.
@@ -63,7 +71,7 @@
     "(bwa-mem2 mem"
     " -t {snakemake.threads}"
     " {extra}"
-    " {snakemake.params.index}"
+    " {index}"
     " {snakemake.input.reads}"
     " | " + pipe_cmd + ") {log}"
 )

bio/bwa/mem/wrapper.py

@@ -16,6 +16,14 @@
 sort_order = snakemake.params.get("sort_order", "coordinate")
 sort_extra = snakemake.params.get("sort_extra", "")
 
+index = None
+if "index" in snakemake.params.keys():
+    index = snakemake.params["index"]
+elif "index" in snakemake.input.keys():
+    index = path.splitext(snakemake.input["index"])[0]
+else:
+    raise ValueError("Could not find BWA index prefix")
+
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
 # Check inputs/arguments.
@@ -61,7 +69,7 @@
     "(bwa mem"
     " -t {snakemake.threads}"
     " {extra}"
-    " {snakemake.params.index}"
+    " {index}"
     " {snakemake.input.reads}"
     " | " + pipe_cmd + ") {log}"
 )