fix: bug with -O being used for gap opening penalty and samtools output directory

bio/minimap2/aligner/meta.yaml

@@ -14,3 +14,4 @@ notes: |
   * The `extra` param allows for additional arguments for minimap2.
   * The `sort` param allows to enable sorting (if output not PAF), and can be either 'none', 'queryname' or 'coordinate'.
   * The `sort_extra` allows for extra arguments for samtools/picard
+  * The `gap_opening` allows for setting gap opening penalty for minimap2.

bio/minimap2/aligner/test/Snakefile

@@ -10,6 +10,7 @@ rule minimap2_paf:
         extra="-x map-pb",  # optional
         sorting="coordinate",  # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
         sort_extra="",  # optional: extra arguments for samtools/picard
+        gap_opening="4" #optional: gap opening penalty for minimap2. Example usage: '4' or '4,24'
     threads: 3
     wrapper:
         "master/bio/minimap2/aligner"
@@ -27,6 +28,7 @@ rule minimap2_sam:
         extra="-x map-pb",  # optional
         sorting="none",  # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
         sort_extra="",  # optional: extra arguments for samtools/picard
+        gap_opening="4" #optional: gap opening penalty for minimap2. Example usage: '4' or '4,24'
     threads: 3
     wrapper:
         "master/bio/minimap2/aligner"
@@ -44,6 +46,7 @@ rule minimap2_sam_sorted:
         extra="-x map-pb",  # optional
         sorting="queryname",  # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
         sort_extra="",  # optional: extra arguments for samtools/picard
+        gap_opening="4" #optional: gap opening penalty for minimap2. Example usage: '4' or '4,24'
     threads: 3
     wrapper:
         "master/bio/minimap2/aligner"
@@ -61,6 +64,7 @@ rule minimap2_bam_sorted:
         extra="-x map-pb",  # optional
         sorting="coordinate",  # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
         sort_extra="",  # optional: extra arguments for samtools/picard
+        gap_opening="4" #optional: gap opening penalty for minimap2. Example usage: '4' or '4,24'
     threads: 3
     wrapper:
         "master/bio/minimap2/aligner"

bio/minimap2/aligner/wrapper.py

@@ -15,6 +15,7 @@
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 sort = snakemake.params.get("sorting", "none")
 sort_extra = snakemake.params.get("sort_extra", "")
+gap_opening = snakemake.params.get("gap_opening", "")
 
 out_ext = infer_out_format(snakemake.output[0])
 
@@ -40,11 +41,15 @@
     else:
         raise ValueError(f"Unexpected value for params.sort: {sort}")
 
+#prepend -O to the command only if gap_opening is specified
+if gap_opening:
+    gap_opening = f"-O {gap_opening}"
 
 shell(
     "(minimap2"
     " -t {snakemake.threads}"
     " {extra} "
+    " {gap_opening} "
     " {snakemake.input.target}"
     " {snakemake.input.query}"
     " {pipe_cmd}"