feat: Regions, samples and targets in get_bcftools_opts (#19)

* new input files added * black formatting Co-authored-by: tdayris <[email protected]>
snakemake · Aug 16, 2022 · e916c8b · e916c8b
1 parent 5c259f5
commit e916c8b
Showing 1 changed file with 38 additions and 6 deletions.
diff --git a/snakemake_wrapper_utils/bcftools.py b/snakemake_wrapper_utils/bcftools.py
@@ -19,6 +19,9 @@ def get_bcftools_opts(
     snakemake,
     parse_threads=True,
     parse_ref=True,
+    parse_region=True,
+    parse_samples=True,
+    parse_targets=True,
     parse_output=True,
     parse_output_format=True,
     parse_memory=True,
@@ -27,7 +30,6 @@ def get_bcftools_opts(
     bcftools_opts = ""
     extra = snakemake.params.get("extra", "")
 
-
     ###############
     ### Threads ###
     ###############
@@ -42,7 +44,6 @@ def get_bcftools_opts(
             else "--threads {}".format(snakemake.threads - 1)
         )
 
-
     ######################
     ### Reference file ###
     ######################
@@ -55,6 +56,41 @@ def get_bcftools_opts(
         if snakemake.input.get("ref"):
             bcftools_opts += f" --fasta-ref {snakemake.input.ref}"
 
+    ####################
+    ### Regions file ###
+    ####################
+    if parse_region:
+        if "--region-file" in extra or "-R" in extra:
+            sys.exit(
+                "You have specified region file (`-R/--regions-file`) in `params.extra`; this is automatically infered from the `regions` input file."
+            )
+
+        if snakemake.input.get("regions"):
+            bcftools_opts += f" --regions-file {snakemake.input.regions}"
+
+    ####################
+    ### Samples file ###
+    ####################
+    if parse_samples:
+        if "-S" in extra or "--samples-file" in extra:
+            sys.exit(
+                "You have specified samples file (`-S/--samples-file`) in `params.extra`; this is automatically infered from the `samples` input file."
+            )
+
+        if snakemake.input.get("samples"):
+            bcftools_opts += f" --samples-file {snakemake.input.samples}"
+
+    ####################
+    ### Targets file ###
+    ####################
+    if parse_targets:
+        if "-T" in extra or "--targets-file" in extra:
+            sys.exit(
+                "You have specified samples file (`-T/--targets-file`) in `params.extra`; this is automatically infered from the `targets` input file."
+            )
+
+        if snakemake.input.get("targets"):
+            bcftools_opts += f" --targets-file {snakemake.input.targets}"
 
     ###################
     ### Output file ###
@@ -66,7 +102,6 @@ def get_bcftools_opts(
             )
         bcftools_opts += f" -o {snakemake.output[0]}"
 
-
     #####################
     ### Output format ###
     #####################
@@ -81,7 +116,6 @@ def get_bcftools_opts(
         )
         bcftools_opts += f" --output-type {out_format}"
 
-
     ##############
     ### Memory ###
     ##############
@@ -98,7 +132,6 @@ def get_bcftools_opts(
         elif "mem_gb" in snakemake.resources.keys():
             bcftools_opts += " --max-mem {}G".format(snakemake.resources["mem_gb"])
 
-
     ################
     ### Temp dir ###
     ################
@@ -107,5 +140,4 @@ def get_bcftools_opts(
             "You have provided `-T/--temp-dir/--temp-prefix` in `params.extra`; please use `resources.tmpdir`."
         )
 
-
     return bcftools_opts