Add additional input arguments to vc-gatk4-hc

docs/CHANGELOG.rst

@@ -32,6 +32,8 @@ Added
 - Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``
 - Use generic permission filters when filtering variants by related models
 - Return only distinct ``VariantExperiment`` objects
+- Add ``--bam-output`` input argument to ``vc-gatk4-hc``
+- Add ``--max-mnp-distance`` input argument to ``vc-gatk4-hc``
 
 
 ===================

resolwe_bio/processes/variant_calling/gatk4_hc.py

@@ -36,7 +36,7 @@ class GatkHaplotypeCaller(Process):
     name = "GATK4 (HaplotypeCaller)"
     category = "GATK"
     process_type = "data:variants:vcf:gatk:hc"
-    version = "1.5.0"
+    version = "1.6.0"
     scheduling_class = SchedulingClass.BATCH
     entity = {"type": "sample"}
     requirements = {
@@ -113,6 +113,33 @@ class Advanced:
                 default=12,
                 description="Set the maximum Java heap size (in GB).",
             )
+            bam_out = BooleanField(
+                label="Output a BAM containing assembled haplotypes.",
+                default=False,
+                description="Output a BAM containing assembled haplotypes. "
+                "Really for debugging purposes only. "
+                "Note that the output here does not include uninformative reads so that not every input read is emitted to the bam. "
+                "Turning on this mode may result in serious performance cost for the caller.",
+            )
+            bam_writer_type = StringField(
+                label="BAM writer type",
+                default="CALLED_HAPLOTYPES",
+                description="The type of BAM output. "
+                "This determines whether HC will write out all of the haplotypes it considered (top 128 max) "
+                "or just the ones that were selected as alleles and assigned to samples.",
+                choices=[
+                    ("CALLED_HAPLOTYPES", "Assigned haplotypes"),
+                    ("ALL_POSSIBLE_HAPLOTYPES", "All considered haplotypes"),
+                    ("NO_HAPLOTYPES", "Do not output haplotypes"),
+                ],
+                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")
 
@@ -121,6 +148,8 @@ class Output:
 
         vcf = FileField(label="VCF file")
         tbi = FileField(label="Tabix index")
+        bam = FileField(label="Alignment file", required=False)
+        bai = FileField(label="BAM file index", required=False)
         species = StringField(label="Species")
         build = StringField(label="Build")
 
@@ -157,6 +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:
@@ -168,6 +199,11 @@ def run(self, inputs, outputs):
             if inputs.advanced.interval_padding:
                 args.extend(["--interval-padding", inputs.advanced.interval_padding])
 
+        if inputs.advanced.bam_out:
+            output_bam = name + ".gatkHC.bam"
+            args.extend(["--bam-output", output_bam])
+            args.extend(["--bam-writer-type", inputs.advanced.bam_writer_type])
+
         return_code, stdout, stderr = Cmd["gatk"]["HaplotypeCaller"][args] & TEE(
             retcode=None
         )
@@ -188,3 +224,9 @@ def run(self, inputs, outputs):
         outputs.tbi = variants_index
         outputs.species = inputs.alignment.output.species
         outputs.build = inputs.alignment.output.build
+        if inputs.advanced.bam_out:
+            output_bai = Path(name + ".gatkHC.bai")
+            renamed_bai = output_bai.with_suffix(".bam.bai")
+            output_bai.rename(renamed_bai)
+            outputs.bam = output_bam
+            outputs.bai = str(renamed_bai)

resolwe_bio/tests/processes/test_variant_calling.py

@@ -193,6 +193,8 @@ def test_gatk_haplotypecaller(self):
                     "soft_clipped": True,
                     "java_gc_threads": 3,
                     "max_heap_size": 7,
+                    "bam_out": True,
+                    "bam_writer_type": "CALLED_HAPLOTYPES",
                 },
             },
         )
@@ -205,6 +207,12 @@ def test_gatk_haplotypecaller(self):
             file_filter=filter_vcf_variable,
             compression="gzip",
         )
+        self.assertFile(
+            gatk_rnaseq, "bam", output_folder / "56GSID_10k.rna-seq.gatkHC.bam"
+        )
+        self.assertFile(
+            gatk_rnaseq, "bai", output_folder / "56GSID_10k.rna-seq.gatkHC.bam.bai"
+        )
 
     @tag_process("snpeff", "snpeff-single")
     def test_snpeff(self):