fixup! Add BAM output option to vc-gatk4-hc

genialis · Dec 10, 2024 · 9170a0e · 9170a0e
1 parent ac9e29c
commit 9170a0e
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Showing 4 changed files with 10 additions and 2 deletions.
diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
@@ -14,7 +14,7 @@ Unreleased
 Added
 -----
 - Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``
-- Add BAM output option to ``vc-gatk4-hc`` 
+- Add ``--bam-output`` 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
@@ -142,7 +142,8 @@ class Output:
 
         vcf = FileField(label="VCF file")
         tbi = FileField(label="Tabix index")
-        bam = FileField(label="BAM file", required=False)
+        bam = FileField(label="Alignment file", required=False)
+        bai = FileField(label="BAM file index", required=False)
         species = StringField(label="Species")
         build = StringField(label="Build")
 
@@ -216,4 +217,8 @@ def run(self, inputs, outputs):
         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)
diff --git a/resolwe_bio/tests/files/haplotypecaller/output/56GSID_10k.rna-seq.gatkHC.bam.bai b/resolwe_bio/tests/files/haplotypecaller/output/56GSID_10k.rna-seq.gatkHC.bam.bai
diff --git a/resolwe_bio/tests/processes/test_variant_calling.py b/resolwe_bio/tests/processes/test_variant_calling.py
@@ -210,6 +210,9 @@ def test_gatk_haplotypecaller(self):
         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):
-Original file line number
+Diff line change
@@ Expand Up / @@ -14,7 +14,7 @@ Unreleased @@
     Added
     -----
     - Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``
-    - Add BAM output option to ``vc-gatk4-hc``
+    - Add ``--bam-output`` input argument to ``vc-gatk4-hc``
     Changed
     -------
@@ Expand Down @@