Added option to disable automatic parsing of some parameters, in case the tool does no support it.

Author: fgvieira

snakemake_wrapper_utils/bcftools.py

@@ -1,75 +1,89 @@
 import sys
 
 
-def get_bcftools_opts(snakemake):
+def get_bcftools_opts(
+    snakemake,
+    parse_threads=True,
+    parse_output_format=True,
+    parse_memory=True,
+    parse_temp_dir=True,
+):
     """Obtain bcftools_opts from output, params, and handle resource definitions in resources."""
     bcftools_opts = ""
     extra = snakemake.params.get("extra", "")
 
     ###############
     ### Threads ###
     ###############
-    if "--threads" in extra:
-        sys.exit(
-            "You have specified number of threads (`--threads`) in params.extra; please use only `threads`."
+    if parse_threads:
+        if "--threads" in extra:
+            sys.exit(
+                "You have specified number of threads (`--threads`) in params.extra; please use only `threads`."
+            )
+        bcftools_opts += (
+            ""
+            if snakemake.threads <= 1
+            else "--threads {}".format(snakemake.threads - 1)
         )
-    bcftools_opts += (
-        "" if snakemake.threads <= 1 else "--threads {}".format(snakemake.threads - 1)
-    )
 
     #####################
     ### Output format ###
     #####################
-    if "-O" in extra or "--output-type" in extra:
-        sys.exit(
-            "You have specified output format (`-O/--output-type`) in params.extra; this is automatically infered from output file extension."
-        )
+    if parse_output_format:
+        if "-O" in extra or "--output-type" in extra:
+            sys.exit(
+                "You have specified output format (`-O/--output-type`) in params.extra; this is automatically infered from output file extension."
+            )
 
-    # Output uncompressed BCF; ignored if output is VCF
-    uncompressed_bcf = snakemake.params.get("uncompressed_bcf", False)
+        # Output uncompressed BCF; ignored if output is VCF
+        uncompressed_bcf = snakemake.params.get("uncompressed_bcf", False)
 
-    output = snakemake.output[0]
-    if output.endswith(".vcf"):
-        out_format = "v"
-    elif output.endswith(".vcf.gz"):
-        out_format = "z"
-    elif output.endswith(".bcf"):
-        if uncompressed_bcf:
-            out_format = "u"
+        output = snakemake.output[0]
+        if output.endswith(".vcf"):
+            out_format = "v"
+        elif output.endswith(".vcf.gz"):
+            out_format = "z"
+        elif output.endswith(".bcf"):
+            if uncompressed_bcf:
+                out_format = "u"
+            else:
+                out_format = "b"
         else:
-            out_format = "b"
-    else:
-        raise ValueError("invalid output file extension ('.vcf', '.vcf.gz', '.bcf').")
+            raise ValueError(
+                "invalid output file extension ('.vcf', '.vcf.gz', '.bcf')."
+            )
 
-    bcftools_opts += f" --output-type {out_format}"
+        bcftools_opts += f" --output-type {out_format}"
 
     ##############
     ### Memory ###
     ##############
-    # Should resources.mem_mb be passed to bcftools (not all tools support this option)
-    bcftools_use_mem = snakemake.params.get("bcftools_use_mem", False)
+    if parse_memory:
+        # Should resources.mem_mb be passed to bcftools (not all tools support this option)
+        bcftools_use_mem = snakemake.params.get("bcftools_use_mem", False)
 
-    if "-m" in extra or "--max-mem" in extra:
-        sys.exit(
-            "You have provided `-m/--max-mem` in params.extra; please only use resources.mem_mb and set params.bcftools_use_mem."
-        )
-    # Getting memory in megabytes, as advised in documentation.
-    if "mem_mb" in snakemake.resources.keys() and bcftools_use_mem:
-        bcftools_opts += " --max-mem {}M".format(snakemake.resources["mem_mb"])
-    # Getting memory in gigabytes, for user convenience. Please prefer the use
-    # of mem_mb over mem_gb as advised in documentation.
-    elif "mem_gb" in snakemake.resources.keys() and bcftools_use_mem:
-        bcftools_opts += " --max-mem {}G".format(snakemake.resources["mem_gb"])
+        if "-m" in extra or "--max-mem" in extra:
+            sys.exit(
+                "You have provided `-m/--max-mem` in params.extra; please only use resources.mem_mb and set params.bcftools_use_mem."
+            )
+        # Getting memory in megabytes, as advised in documentation.
+        if "mem_mb" in snakemake.resources.keys() and bcftools_use_mem:
+            bcftools_opts += " --max-mem {}M".format(snakemake.resources["mem_mb"])
+        # Getting memory in gigabytes, for user convenience. Please prefer the use
+        # of mem_mb over mem_gb as advised in documentation.
+        elif "mem_gb" in snakemake.resources.keys() and bcftools_use_mem:
+            bcftools_opts += " --max-mem {}G".format(snakemake.resources["mem_gb"])
 
     ################
     ### Temp dir ###
     ################
-    if "-T" in extra or "--temp-dir" in extra:
-        sys.exit(
-            "You have provided `-T/--temp-dir` in params.extra; please provide a temp dir as output.bcftools_temp."
-        )
-    # Getting temp directory from output files list
-    if "bcftools_temp" in snakemake.output.keys():
-        bcftools_opts += " --temp-dir {}".format(snakemake.output["bcftools_temp"])
+    if parse_temp_dir:
+        if "-T" in extra or "--temp-dir" in extra:
+            sys.exit(
+                "You have provided `-T/--temp-dir` in params.extra; please provide a temp dir as output.bcftools_temp."
+            )
+        # Getting temp directory from output files list
+        if "bcftools_temp" in snakemake.output.keys():
+            bcftools_opts += " --temp-dir {}".format(snakemake.output["bcftools_temp"])
 
     return bcftools_opts