set primer params

workflow/rules/common.smk

@@ -929,7 +929,7 @@ def get_dgidb_datasources():
 
 def get_filter_params(wc):
     if isinstance(get_panel_primer_input(wc.panel), list):
-        return "-b -f 2"
+        return "-b -F 12"
     return "-b -F 4"
 
 
@@ -949,7 +949,18 @@ def get_shortest_primer_length(primers):
                 [len(p.strip()) for i, p in enumerate(p.readlines()) if i % 2 == 1]
             )
             min_length = min(min_length, min_primer)
-    return min_length - 2
+    return min_length
+
+
+def get_primer_extra(wc, input):
+    extra = fr"-R '@RG\tID:{wc.panel}\tSM:{wc.panel}' -L 100"
+    min_primer_len = get_shortest_primer_length(input.reads)
+    # Check if shortest primer is below default values
+    if min_primer_len < 32:
+        extra += f" -T {min_primer_len - 2}"
+    if min_primer_len < 19:
+        extra += f" -k {min_primer_len}"
+    return extra
 
 
 def get_datavzrd_data(impact="coding"):

workflow/rules/primers.smk

@@ -53,7 +53,7 @@ rule map_primers:
     log:
         "logs/bwa_mem/{panel}.log",
     params:
-        extra=lambda wc, input: rf"-R '@RG\tID:{wc.panel}\tSM:{wc.panel}' -L 100 -T {get_shortest_primer_length(input.reads)}",
+        extra=lambda wc, input: get_primer_extra(wc, input),
         sorting="none",  # Can be 'none', 'samtools' or 'picard'.
         sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
         sort_extra="",  # Extra args for samtools/picard.