feat: GATK FilterMutectCall enhancement (#521)

* [fix] (template): Missing code in wrappers' doc. Error #187 * Wrapper update * Test datasets * Update test case Co-authored-by: tdayris <tdayris@gustaveroussy.fr> Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr>
snakemake · Aug 16, 2022 · eea67d4 · eea67d4
1 parent 2c6b897
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diff --git a/bio/gatk/filtermutectcalls/meta.yaml b/bio/gatk/filtermutectcalls/meta.yaml
@@ -1,14 +1,22 @@
 name: gatk FilterMutectCalls
+url: https://gatk.broadinstitute.org/hc/en-us/articles/360042476952-FilterMutectCalls
 description: |
-  Run gatk FilterMutectCalls.
+  Run gatk FilterMutectCalls to filter variants in a Mutect2 VCF callset.
 authors:
   - Patrik Smeds
   - Filipe G. Vieira
+  - Thibault Dayris
 input:
-  - vcf file
-  - reference genome
+  - vcf: Path to vcf file (pbgzipped, indexed)
+  - ref: Path to reference genome (with .dict file alongside)
+  - aln: Optional path to SAM/BAM/CRAM files
+  - contamination: Optional path to 
+  - segmentation: Optional path to tumor segments
+  - f1r2: Optional path to prior artefact (tar.gz2)
+  - intervels: Optional file to BED intervals
 output:
-  - filtered vcf file
+  - vcf: filtered vcf file
+  - stats: Optional stats from Mutect2
 notes: |
   * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
   * The `extra` param allows for additional program arguments.

diff --git a/bio/gatk/filtermutectcalls/test/Snakefile b/bio/gatk/filtermutectcalls/test/Snakefile
@@ -13,3 +13,25 @@ rule gatk_filtermutectcalls:
         mem_mb=1024,
     wrapper:
         "master/bio/gatk/filtermutectcalls"
+
+
+rule gatk_filtermutectcalls_complete:
+    input:
+        vcf="calls/snvs.vcf",
+        ref="genome.fasta",
+        bam="mapped/a.bam",
+        intervals="intervals.bed",
+        # contamination="", # from gatk CalculateContamination
+        # segmentation="", # from gatk CalculateContamination
+        # f1r2="", # from gatk LearnReadOrientationBias
+    output:
+        vcf="calls/snvs.mutect.filtered.b.vcf",
+    log:
+        "logs/gatk/filter/snvs.log",
+    params:
+        extra="--max-alt-allele-count 3",  # optional arguments, see GATK docs
+        java_opts="",  # optional
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/gatk/filtermutectcalls"
diff --git a/bio/gatk/filtermutectcalls/test/intervals.bed b/bio/gatk/filtermutectcalls/test/intervals.bed
@@ -0,0 +1,2 @@
+ref	3	44
+ref2	8	31
diff --git a/bio/gatk/filtermutectcalls/test/mapped/a.bam b/bio/gatk/filtermutectcalls/test/mapped/a.bam
diff --git a/bio/gatk/filtermutectcalls/test/mapped/a.bam.bai b/bio/gatk/filtermutectcalls/test/mapped/a.bam.bai
diff --git a/bio/gatk/filtermutectcalls/wrapper.py b/bio/gatk/filtermutectcalls/wrapper.py
@@ -12,11 +12,37 @@
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
+
+aln = snakemake.input.get("aln", "")
+if aln:
+    aln = f"--input {aln}"
+
+contamination = snakemake.input.get("contemination_table", "")
+if contamination:
+    contamination = f"--contamination-table {contamination}"
+
+segmentation = snakemake.input.get("segmentation", "")
+if segmentation:
+    segmentation = f"--tumor-segmentation {segmentation}"
+
+f1r2 = snakemake.input.get("f1r2", "")
+if f1r2:
+    f1r2 = f"--orientation-bias-artifact-priors {f1r2}"
+
+intervals = snakemake.input.get("bed", "")
+if intervals:
+    intervals = f"--intervals {intervals}"
+
 with tempfile.TemporaryDirectory() as tmpdir:
     shell(
         "gatk --java-options '{java_opts}' FilterMutectCalls"
         " --variant {snakemake.input.vcf}"
         " --reference {snakemake.input.ref}"
+        " {aln}"  # BAM/SAM/CRAM file containing reads
+        " {contamination}"  # Tables containing contamination information
+        " {segmentation}"  # Tumor segments' minor allele fractions
+        " {f1r2}"  # .tar.gz files containing tables of prior artifact
+        " {intervals}"  # Genomic intervals over which to operate
         " {extra}"
         " --tmp-dir {tmpdir}"
         " --output {snakemake.output.vcf}"

diff --git a/test.py b/test.py
@@ -3423,6 +3423,18 @@ def test_gatk_filtermutectcalls():
         ],
     )
 
+    run(
+        "bio/gatk/filtermutectcalls",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "calls/snvs.mutect.filtered.b.vcf",
+            "--use-conda",
+            "-F",
+        ],
+    )
+
 
 @skip_if_not_modified
 def test_gatk_selectvariants():