Java (multiple tools) -Xmx parameter

bio/gatk/applybqsr/environment.yaml

@@ -4,4 +4,5 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
-  - openjdk =8
+  - openjdk =8
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/applybqsr/test/Snakefile

@@ -11,5 +11,11 @@ rule gatk_applybqsr:
     params:
         extra="",  # optional
         java_opts="", # optional
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     wrapper:
         "master/bio/gatk/applybqsr"

bio/gatk/applybqsr/wrapper.py

@@ -5,13 +5,15 @@
 
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 extra = snakemake.params.get("extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
 shell(
-    "gatk --java-options '{java_opts}' ApplyBQSR {extra} -R {snakemake.input.ref} -I {snakemake.input.bam} "
+    "gatk --java-options '{java_opts}' ApplyBQSR {extra} "
+    "-R {snakemake.input.ref} -I {snakemake.input.bam} "
     "--bqsr-recal-file {snakemake.input.recal_table} "
     "-O {snakemake.output.bam} {log}"
 )

bio/gatk/baserecalibrator/environment.yaml

@@ -4,4 +4,5 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
-  - openjdk =8
+  - openjdk =8
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/baserecalibrator/test/Snakefile

@@ -11,5 +11,11 @@ rule gatk_baserecalibrator:
     params:
         extra="",  # optional
         java_opts="", # optional
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     wrapper:
         "master/bio/gatk/baserecalibrator"

bio/gatk/baserecalibrator/wrapper.py

@@ -5,9 +5,10 @@
 
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 extra = snakemake.params.get("extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 known = snakemake.input.get("known", "")

bio/gatk/baserecalibratorspark/environment.yaml

@@ -4,4 +4,5 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
-  - openjdk =8
+  - openjdk =8
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/baserecalibratorspark/test/Snakefile

@@ -14,6 +14,12 @@ rule gatk_baserecalibratorspark:
         #spark_runner="",  # optional, local by default
         #spark_master="",  # optional
         #spark_extra="", # optional
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     threads: 8
     wrapper:
         "master/bio/gatk/baserecalibratorspark"

bio/gatk/baserecalibratorspark/wrapper.py

@@ -5,14 +5,15 @@
 
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 extra = snakemake.params.get("extra", "")
 spark_runner = snakemake.params.get("spark_runner", "LOCAL")
 spark_master = snakemake.params.get(
     "spark_master", "local[{}]".format(snakemake.threads)
 )
 spark_extra = snakemake.params.get("spark_extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 known = snakemake.input.get("known", "")

bio/gatk/combinegvcfs/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/combinegvcfs/test/Snakefile

@@ -9,5 +9,11 @@ rule genotype_gvcfs:
     params:
         extra="",  # optional
         java_opts="",  # optional
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     wrapper:
         "master/bio/gatk/combinegvcfs"

bio/gatk/combinegvcfs/wrapper.py

@@ -7,10 +7,12 @@
 import os
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 
 extra = snakemake.params.get("extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
+
 gvcfs = list(map("-V {}".format, snakemake.input.gvcfs))
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)

bio/gatk/genotypegvcfs/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/genotypegvcfs/test/Snakefile

@@ -9,5 +9,11 @@ rule genotype_gvcfs:
     params:
         extra="",  # optional
         java_opts="", # optional
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     wrapper:
         "master/bio/gatk/genotypegvcfs"

bio/gatk/genotypegvcfs/wrapper.py

@@ -7,10 +7,11 @@
 import os
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 
 extra = snakemake.params.get("extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 shell(

bio/gatk/haplotypecaller/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/haplotypecaller/test/Snakefile

@@ -11,5 +11,11 @@ rule haplotype_caller:
     params:
         extra="",  # optional
         java_opts="", # optional
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     wrapper:
         "master/bio/gatk/haplotypecaller"

bio/gatk/haplotypecaller/wrapper.py

@@ -7,13 +7,15 @@
 import os
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 known = snakemake.input.get("known", "")
 if known:
     known = "--dbsnp " + known
 
 extra = snakemake.params.get("extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
+
 bams = snakemake.input.bam
 if isinstance(bams, str):
     bams = [bams]

bio/gatk/mutect/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/mutect/test/Snakefile

@@ -8,6 +8,12 @@ rule mutect2:
         "Testing Mutect2 with {wildcards.sample}"
     threads:
         1
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     log:
         "logs/mutect_{sample}.log"
     wrapper:

bio/gatk/mutect/wrapper.py

@@ -7,13 +7,15 @@
 
 from snakemake.shell import shell
 from snakemake.utils import makedirs
+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)
 
 shell(
-    "gatk Mutect2 "  # Tool and its subprocess
+    "gatk --java-options '{java_opts}' Mutect2 "  # Tool and its subprocess
     "--input {snakemake.input.map} "  # Path to input mapping file
     "--output {snakemake.output.vcf} "  # Path to output vcf file
     "--reference {snakemake.input.fasta} "  # Path to reference fasta file

bio/gatk/selectvariants/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/selectvariants/test/Snakefile

@@ -8,6 +8,12 @@ rule gatk_select:
         "logs/gatk/select/snvs.log"
     params:
         extra="--select-type-to-include SNP",  # optional filter arguments, see GATK docs
-        java_opts="", # optional 
+        java_opts="", # optional
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     wrapper:
         "master/bio/gatk/selectvariants"

bio/gatk/selectvariants/wrapper.py

@@ -5,9 +5,10 @@
 
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 extra = snakemake.params.get("extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 shell(

bio/gatk/splitncigarreads/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/splitncigarreads/test/Snakefile

@@ -9,5 +9,11 @@ rule splitncigarreads:
     params:
         extra="",  # optional
         java_opts="",  # optional
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     wrapper:
         "master/bio/gatk/splitncigarreads"

bio/gatk/splitncigarreads/wrapper.py

@@ -6,9 +6,10 @@
 import os
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 extra = snakemake.params.get("extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 shell(

bio/gatk/variantfiltration/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/variantfiltration/test/Snakefile

@@ -10,5 +10,11 @@ rule gatk_filter:
         filters={"myfilter": "AB < 0.2 || MQ0 > 50"},
         extra="",  # optional arguments, see GATK docs
         java_opts="", # optional
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     wrapper:
         "master/bio/gatk/variantfiltration"

bio/gatk/variantfiltration/wrapper.py

@@ -5,9 +5,11 @@
 
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 extra = snakemake.params.get("extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
+
 filters = [
     "--filter-name {} --filter-expression '{}'".format(name, expr.replace("'", "\\'"))
     for name, expr in snakemake.params.filters.items()

bio/gatk/variantrecalibrator/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - defaults
 dependencies:
   - gatk4 ==4.1.4.1
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/variantrecalibrator/test/Snakefile

@@ -19,7 +19,7 @@ rule haplotype_caller:
         g1k=gatk_bundle("1000G_phase1.snps.high_confidence.hg38.vcf.gz"),
         dbsnp=gatk_bundle("Homo_sapiens_assembly38.dbsnp138.vcf.gz"),
         # use aux to e.g. download other necessary file
-        aux=[gatk_bundle("hapmap_3.3.hg38.sites.vcf.gz.tbi"), 
+        aux=[gatk_bundle("hapmap_3.3.hg38.sites.vcf.gz.tbi"),
              gatk_bundle("1000G_omni2.5.hg38.sites.vcf.gz.tbi"),
              gatk_bundle("1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi"),
              gatk_bundle("Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi")]
@@ -38,5 +38,11 @@ rule haplotype_caller:
         annotation=["QD", "FisherStrand"],  # which fields to use with -an (see VariantRecalibrator docs)
         extra="",  # optional
         java_opts="", # optional
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    resources:
+        mem_mb=1024
     wrapper:
         "master/bio/gatk/haplotypecaller"

bio/gatk/variantrecalibrator/wrapper.py

@@ -7,10 +7,11 @@
 import os
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 
 extra = snakemake.params.get("extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
 
 
 def fmt_res(resname, resparams):

bio/gatk3/baserecalibrator/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - defaults
 dependencies:
   - gatk ==3.8
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk3/baserecalibrator/wrapper.py

@@ -6,9 +6,10 @@
 import os
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
 extra = snakemake.params.get("extra", "")
-java_opts = snakemake.params.get("java_opts", "")
+java_opts = get_java_opts(snakemake)
 
 input_bam = snakemake.input.bam
 input_known = snakemake.input.known

bio/gatk3/indelrealigner/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - defaults
 dependencies:
   - gatk ==3.8
+  - snakemake-wrapper-utils ==0.1.3