feat: gatk Learnreadorientationmodel

bio/gatk/learnreadorientationmodel/environment.yaml

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

bio/gatk/learnreadorientationmodel/meta.yaml

@@ -0,0 +1,12 @@
+name: GATK LearnOrientationModel
+url: https://gatk.broadinstitute.org/hc/en-us/articles/4405451237147-LearnReadOrientationModel
+description: Get the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter
+authors:
+  - Thibault Dayris
+input:
+  - f1r2: Path to one or multiple f1r2 files
+output:
+  - Path to tar.gz of artifact prior tables
+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.

bio/gatk/learnreadorientationmodel/test/Snakefile

@@ -0,0 +1,13 @@
+rule test_gatk_learnreadorientationmodel:
+    input:
+        f1r2="f1r2.tar.gz",
+    output:
+        "artifacts_prior.tar.gz",
+    resources:
+        mem_mb=1024,
+    params:
+        extra="",
+    log:
+        "learnreadorientationbias.log",
+    wrapper:
+        "master/bio/gatk/learnreadorientationmodel"

bio/gatk/learnreadorientationmodel/wrapper.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+"""Snakemake wrapper for GATK4 LearnReadOrientationModel"""
+
+__author__ = "Thibault Dayris"
+__copyright__ = "Copyright 2022, Dayris Thibault"
+__email__ = "[email protected]"
+__license__ = "MIT"
+
+import tempfile
+from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
+java_opts = get_java_opts(snakemake)
+
+f1r2 = "--input "
+if isinstance(snakemake.input["f1r2"], list):
+    # Case user provided a list of archives
+    f1r2 += "--input ".join(snakemake.input["f1r2"])
+else:
+    # Case user provided a single archive as a string
+    f1r2 += snakemake.input["f1r2"]
+
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "gatk --java-options '{java_opts}' LearnReadOrientationModel"  # Tool and its subprocess
+        " {f1r2}"  # Path to input mapping file
+        " {extra}"  # Extra parameters
+        " --tmp-dir {tmpdir}"
+        " --output {snakemake.output[0]}"  # Path to output vcf file
+        " {log}"  # Logging behaviour
+    )

test.py

@@ -3395,6 +3395,14 @@ def test_gatk_mutect():
     )
 
 
+@skip_if_not_modified
+def test_gatk_learn_read_orientation():
+    run(
+        "bio/gatk/learnreadorientationmodel",
+        ["snakemake", "--cores", "1", "--use-conda"]
+    )
+
+
 @skip_if_not_modified
 def test_gatk_mutect_bam():
     run(