feat: added GATK variantAnnotator wrapper (#462)

* Added GATK variantAnnotator wrapper

* BGziped VCF

* Fixed typo

* Added intervals to example Snakefile

bio/gatk/variantannotator/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - gatk4 =4.2
+  - snakemake-wrapper-utils =0.3

bio/gatk/variantannotator/meta.yaml

@@ -0,0 +1,16 @@
+name: gatk VariantAnnotator
+description: |
+  Run gatk VariantAnnotator.
+authors:
+  - Filipe G. Vieira
+input:
+  - VCF file
+  - BAM file
+  - reference genome
+  - VCF of known variation
+output:
+  - annotated VCF file
+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.
+  * For more information see, https://gatk.broadinstitute.org/hc/en-us/articles/4418054223003-VariantAnnotator

bio/gatk/variantannotator/test/Snakefile

@@ -0,0 +1,18 @@
+rule gatk_annotator:
+    input:
+        vcf="calls/snvs.vcf.gz",
+        aln="mapped/a.bam",
+        ref="genome.fasta",
+        db="calls/snvs.vcf.gz",
+#        intervals="targets.bed",
+    output:
+        vcf="snvs.annot.vcf",
+    log:
+        "logs/gatk/annotator/snvs.log",
+    params:
+        extra="--resource-allele-concordance -A Coverage --expression db.END",
+        java_opts="",  # optional
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/gatk/variantannotator"

bio/gatk/variantannotator/test/genome.dict

@@ -0,0 +1,3 @@
+@HD	VN:1.5
+@SQ	SN:ref	LN:45	M5:7a66cae8ab14aef8d635bc80649e730b	UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta
+@SQ	SN:ref2	LN:40	M5:1636753510ec27476fdd109a6684680e	UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta

bio/gatk/variantannotator/test/genome.fasta

@@ -0,0 +1,4 @@
+>ref
+AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
+>ref2
+aggttttataaaacaattaagtctacagagcaactacgcg

bio/gatk/variantannotator/test/genome.fasta.fai

@@ -0,0 +1,2 @@
+ref	45	5	45	46
+ref2	40	57	40	41

bio/gatk/variantannotator/wrapper.py

@@ -0,0 +1,52 @@
+__author__ = "Filipe G. Vieira"
+__copyright__ = "Copyright 2022, Filipe G. Vieira"
+__license__ = "MIT"
+
+import tempfile
+from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
+
+extra = snakemake.params.get("extra", "")
+java_opts = get_java_opts(snakemake)
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+
+input = snakemake.input.get("aln", "")
+if input:
+    input = f"--input {input}"
+
+reference = snakemake.input.get("ref", "")
+if reference:
+    reference = f"--reference {reference}"
+
+dbsnp = snakemake.input.get("known", "")
+if dbsnp:
+    dbsnp = f"--dbsnp {dbsnp}"
+
+intervals = snakemake.input.get("intervals", "")
+if not intervals:
+    intervals = snakemake.params.get("intervals", "")
+if intervals:
+    intervals = "--intervals {}".format(intervals)
+
+resources = [
+    f"--resource:{name} {file}"
+    for name, file in snakemake.input.items()
+    if name not in ["vcf", "aln", "ref", "known", "intervals"]
+]
+
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "gatk --java-options '{java_opts}' VariantAnnotator"
+        " --variant {snakemake.input.vcf}"
+        " {input}"
+        " {reference}"
+        " {dbsnp}"
+        " {intervals}"
+        " {resources}"
+        " {extra}"
+        " --tmp-dir {tmpdir}"
+        " --output {snakemake.output.vcf}"
+        " {log}"
+    )

bio/gatk/variantfiltration/test/Snakefile

@@ -2,6 +2,7 @@ rule gatk_filter:
     input:
         vcf="calls/snvs.vcf",
         ref="genome.fasta",
+#        intervals="targets.bed",
     output:
         vcf="calls/snvs.filtered.vcf",
     log:

bio/gatk/variantfiltration/wrapper.py

@@ -9,20 +9,29 @@
 
 extra = snakemake.params.get("extra", "")
 java_opts = get_java_opts(snakemake)
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
 
 filters = [
     "--filter-name {} --filter-expression '{}'".format(name, expr.replace("'", "\\'"))
     for name, expr in snakemake.params.filters.items()
 ]
 
-log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+intervals = snakemake.input.get("intervals", "")
+if not intervals:
+    intervals = snakemake.params.get("intervals", "")
+if intervals:
+    intervals = "--intervals {}".format(intervals)
+
 
 with tempfile.TemporaryDirectory() as tmpdir:
     shell(
         "gatk --java-options '{java_opts}' VariantFiltration"
         " --variant {snakemake.input.vcf}"
         " --reference {snakemake.input.ref}"
         " {filters}"
+        " {intervals}"
         " {extra}"
         " --tmp-dir {tmpdir}"
         " --output {snakemake.output.vcf}"

test.py

@@ -3133,6 +3133,14 @@ def test_gatk_selectvariants():
     )
 
 
+@skip_if_not_modified
+def test_gatk_variantannotator():
+    run(
+        "bio/gatk/variantannotator",
+        ["snakemake", "--cores", "1", "snvs.annot.vcf", "--use-conda", "-F"],
+    )
+
+
 @skip_if_not_modified
 def test_gatk_variantfiltration():
     run(