feat: add option to disable normal hardfilter

BALSAMIC/commands/config/case.py

@@ -22,6 +22,7 @@
     OPTION_CASE_ID,
     OPTION_CLINICAL_SNV_OBSERVATIONS,
     OPTION_CLINICAL_SV_OBSERVATIONS,
+    OPTION_SOFT_FILTER_NORMAL,
     OPTION_EXOME,
     OPTION_FASTQ_PATH,
     OPTION_GENDER,
@@ -77,6 +78,7 @@
 @OPTION_CASE_ID
 @OPTION_CLINICAL_SNV_OBSERVATIONS
 @OPTION_CLINICAL_SV_OBSERVATIONS
+@OPTION_SOFT_FILTER_NORMAL
 @OPTION_EXOME
 @OPTION_FASTQ_PATH
 @OPTION_GENDER
@@ -121,6 +123,7 @@ def case_config(
     pon_cnn: Path,
     sentieon_install_dir: Path,
     sentieon_license: str,
+    soft_filter_normal: bool,
     swegen_snv: Path,
     swegen_sv: Path,
     tumor_sample_name: str,
@@ -193,6 +196,7 @@ def case_config(
         },
         analysis={
             "case_id": case_id,
+            "soft_filter_normal": soft_filter_normal,
             "gender": gender,
             "analysis_dir": analysis_dir,
             "fastq_path": analysis_fastq_dir,

BALSAMIC/commands/options.py

@@ -141,6 +141,13 @@
     help="Cluster configuration JSON file path",
 )
 
+OPTION_SOFT_FILTER_NORMAL = click.option(
+    "--soft-filter-normal",
+    is_flag=True,
+    default=False,
+    help="Flag to disable hard-filtering on presence of variants in matched normal sample",
+)
+
 OPTION_CLUSTER_MAIL = click.option(
     "--mail-user",
     type=click.STRING,