feat: GATK utils for common IO files (#39)

* GATK utils for common IO files

* Black formatting

* Default set to False

* Typo

* inferred with two r

* Code format

* Code reformat

* Code reformat

* Rename ref_dict

---------

Co-authored-by: tdayris <[email protected]>
Co-authored-by: Filipe G. Vieira <[email protected]>

Author: tdayris

snakemake_wrapper_utils/gatk.py

@@ -0,0 +1,99 @@
+import sys
+from snakemake_wrapper_utils.snakemake import is_arg
+
+
+def get_gatk_opts(
+    snakemake,
+    parse_arg_file=False,
+    parse_bam_index=False,
+    parse_bam_md5=False,
+    parse_vcf_index=False,
+    parse_vcf_md5=False,
+    parse_ref=False,
+    parse_ref_dict=False,
+    param_name="extra",
+):
+    """Obtain gatk_opts from input, output, params"""
+
+    gatk_opts = ""
+    extra = snakemake.params.get(param_name, "")
+
+    ##########################
+    ### Configuration file ###
+    ##########################
+
+    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`."
+            )
+
+        # 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)
+
+            gatk_opts += f"--argument_file {arg_file}"
+
+    ######################
+    ### Reference file ###
+    ######################
+
+    if parse_ref:
+        if is_arg("-R", extra) or is_arg("--reference", extra):
+            sys.exit(
+                "You have specified reference file (`-R,--reference`) in `params.extra`; this is automatically inferred from `input.ref`."
+            )
+        ref = snakemake.input.get("ref")
+        if ref:
+            gatk_opts += f" --reference {ref}"
+
+    if parse_ref_dict:
+        if is_arg("--sequence-dictionary", extra):
+            sys.exit(
+                "You have specified reference sequence dictionary (`--sequence-dictionary`) in `params.extra`; this is automatically inferred from `input.dict`."
+            )
+        dict = snakemake.input.get("dict", "")
+        if dict:
+            gatk_opts += f" --sequence-dictionary {dict}"
+
+    ###########################
+    ### Optional BAM output ###
+    ###########################
+    if parse_bam_index:
+        if is_arg("--create-output-bam-index", extra) or is_arg("-OBI", extra):
+            sys.exit(
+                "You have specified bam index creation (`-OBI,--create-output-bam-index`) in `params.extra`; this is automatically inferred from `output.bam_bai`."
+            )
+        if snakemake.output.get("bam_bai"):
+            gatk_opts += " --create-output-bam-index"
+
+    if parse_bam_md5:
+        if is_arg("--create-output-bam-md5", extra) or is_arg("-OBM", extra):
+            sys.exit(
+                "You have specified bam MD5-sum creation (`-OBM,--create-output-bam-md5`) in `params.extra`; this is automatically inferred from `output.bam_md5`."
+            )
+        if snakemake.output.get("bam_md5"):
+            gatk_opts += " --create-output-bam-md5"
+
+    ###########################
+    ### Optional VCF output ###
+    ###########################
+    if parse_vcf_index:
+        if is_arg("--create-output-variant-index", extra) or is_arg("-OVI", extra):
+            sys.exit(
+                "You have specified VCF index creation (`--OVI,--create-output-variant-index`) in `params.extra`; this is automatically inferred from `output.vcf_idx`."
+            )
+        if snakemake.output.get("vcf_idx"):
+            gatk_opts += " --create-output-variant-index "
+
+    if parse_vcf_md5:
+        if is_arg("--create-output-variant-md5", extra) or is_arg("-OVM", extra):
+            sys.exit(
+                "You have specified VCF MD5-sum creation (`--OVI,--create-output-variant-index`) in `params.extra`; this is automatically inferred from `output.vcf_md5`."
+            )
+        if snakemake.output.get("vcf_md5"):
+            gatk_opts += " --create-output-variant-md5 "
+
+    return gatk_opts