Add --max-mnp-distance input argument to vc-gatk4-hc

genialis · Dec 10, 2024 · 46c6576 · 46c6576
1 parent 9170a0e
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diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
@@ -15,6 +15,7 @@ Added
 -----
 - Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``
 - Add ``--bam-output`` input argument to ``vc-gatk4-hc``
+- Add ``--max-mnp-distance`` input argument to ``vc-gatk4-hc``
 
 Changed
 -------

diff --git a/resolwe_bio/processes/variant_calling/gatk4_hc.py b/resolwe_bio/processes/variant_calling/gatk4_hc.py
@@ -134,6 +134,12 @@ class Advanced:
                 ],
                 disabled="!bam_out",
             )
+            max_mnp_distance = IntegerField(
+                label="Max MNP distance",
+                default=0,
+                description="Two or more phased substitutions separated by this distance or less are merged into MNPs. "
+                "Set 0 to disable.",
+            )
 
         advanced = GroupField(Advanced, label="Advanced options")
 
@@ -180,6 +186,8 @@ def run(self, inputs, outputs):
             inputs.stand_call_conf,
             "--tmp-dir",
             TMPDIR,
+            "--max-mnp-distance",
+            inputs.advanced.max_mnp_distance,
         ]
 
         if inputs.advanced.soft_clipped:
-Original file line number
+Diff line change
@@ Expand Up / @@ -15,6 +15,7 @@ Added @@
     -----
     - Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``
     - Add ``--bam-output`` input argument to ``vc-gatk4-hc``
+    - Add ``--max-mnp-distance`` input argument to ``vc-gatk4-hc``
     Changed
     -------
@@ Expand Down @@