Merge pull request #5 from fgvieira/samtools

Added samtools utils to parse threads, and output format

Author: johanneskoester

snakemake_wrapper_utils/samtools.py

@@ -0,0 +1,37 @@
+import sys
+from os import path
+
+
+def get_samtools_opts(snakemake, parse_threads=True, parse_output_format=True):
+    """Obtain samtools_opts from output, params, and handle resource definitions in resources."""
+    samtools_opts = ""
+    extra = snakemake.params.get("extra", "")
+
+    ###############
+    ### Threads ###
+    ###############
+    if parse_threads:
+        if "-@" in extra or "--threads" in extra:
+            sys.exit(
+                "You have specified number of threads (`-@/--threads`) in params.extra; please use only `threads`."
+            )
+            samtools_opts += (
+                ""
+                if snakemake.threads <= 1
+                else "--threads {}".format(snakemake.threads - 1)
+            )
+
+    #####################
+    ### Output format ###
+    #####################
+    if parse_output_format:
+        if "-O" in extra or "--output-fmt" in extra:
+            sys.exit(
+                "You have specified output format (`-O/--output-fmt`) in params.extra; this is automatically infered from output file extension."
+            )
+
+        out_name, out_ext = path.splitext(snakemake.output[0])
+        out_ext = out_ext[1:].upper()
+        samtools_opts += f" --output-fmt {out_ext}"
+
+    return samtools_opts