feat: Read and write variant files

snakemake_wrapper_utils/bcftools.py

@@ -144,3 +144,63 @@ def get_bcftools_opts(
         )
 
     return bcftools_opts
+
+
+def read_write_variants(snakemake, variant_key_name="call"):
+    """Obtain command lines to read gzipped VCF or BCF files and path to named pipes"""
+    if isinstance(variant_key_name, int):
+        in_call = snakemake.input[0]
+    else:
+        in_call = snakemake.input.get(variant_key_name)
+    min_threads = 1
+    if not in_call:
+        raise KeyError(
+            f"Could not find {variant_key_name} within available snakemake input keys"
+        )
+
+    command_lines = ""
+    input_file_name = in_call
+    if str(in_call).endswith((".gz", ".bcf")):
+        input_file_name = f"{in_call}.snakemake_wrapper_utils_read_variants.vcf"
+        min_threads += 1
+
+        # Case there is a comparison:
+        bcftools_opts = get_bcftools_opts(
+            snakemake,
+            parse_threads=False,  # Since no additional threads are required for reading
+            parse_output=False,  # Since we do not write to any file
+            parse_output_format=False,
+        )
+
+        # Create named pipe
+        command_lines += str(
+            f"mkfifo {input_file_name} ; "
+            f"bcftools view {bcftools_opts} {in_call} > {input_file_name} & "
+        )
+
+    if isinstance(variant_key_name, int):
+        out_call = snakemake.output[variant_key_name]
+    else:
+        out_call = snakemake.output.get(variant_key_name)
+    output_file_name = out_call
+    if not out_call:
+        raise KeyError(
+            f"Could not find {variant_key_name} within available snakemake output keys"
+        )
+
+    if str(out_call).endswith((".gz", ".bcf")):
+        output_file_name = f"{out_call}.snakemake_wrapper_utils_write_variants.vcf"
+        min_threads += 1
+
+        # This time, we include threading and output formats
+        bcftools_opts = get_bcftools_opts(snakemake)
+        command_lines += str(
+            f"mkfifo {output_file_name} ; "
+            f"bcftools view {bcftools_opts} {output_file_name} & "
+        )
+
+    if snakemake.threads < min_threads:
+        raise ValueError(
+            f"At least {min_threads} threads required, got {snakemake.threads}"
+        )
+    return command_lines, input_file_name, output_file_name

snakemake_wrapper_utils/gatk.py

@@ -25,16 +25,16 @@ def get_gatk_opts(
     if parse_arg_file:
         if is_arg("--arguments_file", extra):
             sys.exit(
-                "You have specified an argument file (`--argument_file`) in `params.extra`; this is automatically inferred from `input.arg_file`."
+                "You have specified an argument file (`--arguments_file`) in `params.extra`; this is automatically inferred from `input.arg_file`."
             )
 
         # Multiple argument files can be provided. Order matters.
         arg_file = snakemake.input.get("arg_file", "")
         if arg_file:
             if isinstance(arg_file, list):
-                arg_file = " --argument_file ".join(arg_file)
+                arg_file = " --arguments_file ".join(arg_file)
 
-            gatk_opts += f" --argument_file {arg_file}"
+            gatk_opts += f" --arguments_file {arg_file}"
 
     ######################
     ### Reference file ###