fix: use new java memory overhead utils (#1150)

### Description This updates all uses of `snakemake-wrapper-utils` to the latest version `0.5.2`. Mostly, to automatically have all the wrappers that use the `get_java_opts()` function reserve 20% of the reserved memory for overhead of the JVM. In some cases, I have increased that default, where the documentation indicated that the overhead is usually larger. And in some cases, I switched the specification in the example Snakefile from `mem_gb` to the canonical `mem_mb`, which is sure to be interpreted correctly for job submissions on cluster systems. ### QC  * [x] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, * either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, * rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), * all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), * wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), * all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), * `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, * temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), * the `meta.yaml` contains a link to the documentation of the respective tool or command, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).
snakemake · Mar 23, 2023 · d15d5f5 · d15d5f5
1 parent cb1372b
commit d15d5f5
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diff --git a/bio/bazam/environment.yaml b/bio/bazam/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bazam =1.0.1
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bazam/test/Snakefile b/bio/bazam/test/Snakefile
@@ -5,7 +5,9 @@ rule bazam_interleaved:
     output:
         reads="results/reads/{sample}.fastq.gz",
     resources:
-        mem_mb=12000,
+        # suggestion according to:
+        # https://github.com/ssadedin/bazam/blob/c5988daf4cda4492e3d519c94f2f1e2022af5efe/README.md?plain=1#L46-L55
+        mem_mb=lambda wildcards, input: max([0.2 * input.size_mb, 200]),
     log:
         "logs/bazam/{sample}.log",
     wrapper:
@@ -21,7 +23,9 @@ rule bazam_separated:
         r1="results/reads/{sample}.r1.fastq.gz",
         r2="results/reads/{sample}.r2.fastq.gz",
     resources:
-        mem_mb=12000,
+        # suggestion according to:
+        # https://github.com/ssadedin/bazam/blob/c5988daf4cda4492e3d519c94f2f1e2022af5efe/README.md?plain=1#L46-L55
+        mem_mb=lambda wildcards, input: max([0.4 * input.size_mb, 200]),
     log:
         "logs/bazam/{sample}.log",
     wrapper:

diff --git a/bio/bbtools/bbduk/environment.yaml b/bio/bbtools/bbduk/environment.yaml
@@ -4,5 +4,5 @@ channels:
   - nodefaults
 dependencies:
   - bbmap =39.01
+  - snakemake-wrapper-utils =0.5.2
   - python =3.11.0
-  - snakemake-wrapper-utils =0.5.0
diff --git a/bio/bbtools/bbduk/test/Snakefile b/bio/bbtools/bbduk/test/Snakefile
@@ -11,6 +11,8 @@ rule bbduk_se:
         "logs/bbduk/se/{sample}.log"
     params:
         extra = lambda w, input: "ref={},adapters,artifacts ktrim=r k=23 mink=11 hdist=1 tpe tbo trimpolygright=10 minlen=25 maxns=30 entropy=0.5 entropywindow=50 entropyk=5".format(input.adapters),
+    resources:
+        mem_mb=4000,
     threads: 7
     wrapper:
         "master/bio/bbtools/bbduk"
@@ -29,6 +31,8 @@ rule bbduk_pe:
         "logs/bbduk/pe/{sample}.log"
     params:
         extra = lambda w, input: "ref={},adapters,artifacts ktrim=r k=23 mink=11 hdist=1 tpe tbo trimpolygright=10 minlen=25 maxns=30 entropy=0.5 entropywindow=50 entropyk=5".format(input.adapters),
+    resources:
+        mem_mb=4000,
     threads: 7
     wrapper:
         "master/bio/bbtools/bbduk"
diff --git a/bio/bcftools/call/environment.yaml b/bio/bcftools/call/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bcftools/concat/environment.yaml b/bio/bcftools/concat/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bcftools/index/environment.yaml b/bio/bcftools/index/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bcftools/merge/environment.yaml b/bio/bcftools/merge/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bcftools/mpileup/environment.yaml b/bio/bcftools/mpileup/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bcftools/norm/environment.yaml b/bio/bcftools/norm/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bcftools/norm/test/Snakefile b/bio/bcftools/norm/test/Snakefile
@@ -3,7 +3,7 @@ rule norm_vcf:
         "{prefix}.bcf",
         #ref="genome.fasta"  # optional reference (will be translated into the -f option)
     output:
-        "{prefix}.norm.vcf", # can also be .bcf, corresponding --output-type parameter is inferred automatically
+        "{prefix}.norm.vcf",  # can also be .bcf, corresponding --output-type parameter is inferred automatically
     log:
         "{prefix}.norm.log",
     params:

diff --git a/bio/bcftools/reheader/environment.yaml b/bio/bcftools/reheader/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bcftools/sort/environment.yaml b/bio/bcftools/sort/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bcftools/stats/environment.yaml b/bio/bcftools/stats/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bcftools/view/environment.yaml b/bio/bcftools/view/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bellerophon/environment.yaml b/bio/bellerophon/environment.yaml
@@ -5,4 +5,4 @@ channels:
 dependencies:
   - bellerophon =1.0
   - samtools =1.16.1
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bowtie2/align/environment.yaml b/bio/bowtie2/align/environment.yaml
@@ -5,4 +5,4 @@ channels:
 dependencies:
   - bowtie2 =2.5.0
   - samtools =1.16.1
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bustools/sort/environment.yaml b/bio/bustools/sort/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - bustools =0.42.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bwa-mem2/mem/environment.yaml b/bio/bwa-mem2/mem/environment.yaml
@@ -6,4 +6,4 @@ dependencies:
   - bwa-mem2 =2.2.1
   - samtools =1.16.1
   - picard-slim =3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/bwa/mem/environment.yaml b/bio/bwa/mem/environment.yaml
@@ -6,4 +6,4 @@ dependencies:
   - bwa =0.7.17
   - samtools =1.16.1
   - picard-slim =2.27.4
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/delly/environment.yaml b/bio/delly/environment.yaml
@@ -5,4 +5,4 @@ channels:
 dependencies:
   - delly =1.1.6
   - bcftools =1.16
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/dragmap/align/environment.yaml b/bio/dragmap/align/environment.yaml
@@ -6,4 +6,4 @@ dependencies:
   - dragmap =1.2
   - samtools =1.14
   - picard =2.26
-  - snakemake-wrapper-utils =0.3
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/fgbio/annotatebamwithumis/environment.yaml b/bio/fgbio/annotatebamwithumis/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - fgbio =2.1.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/fgbio/annotatebamwithumis/test/Snakefile b/bio/fgbio/annotatebamwithumis/test/Snakefile
@@ -6,7 +6,10 @@ rule AnnotateBam:
         "mapped/{sample}.annotated.bam",
     params: ""
     resources:
-        mem_gb="4" # memory to be given to fgbio
+        # suggestion assuming unsorted input, so that memory should
+        # be proportional to input size:
+        # https://fulcrumgenomics.github.io/fgbio/tools/latest/AnnotateBamWithUmis.html
+        mem_mb=lambda wildcards, input: max([input.size_mb * 1.3, 200])
     log:
         "logs/fgbio/annotate_bam/{sample}.log",
     wrapper:

diff --git a/bio/gatk/applybqsr/environment.yaml b/bio/gatk/applybqsr/environment.yaml
@@ -4,5 +4,5 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
   - samtools =1.16.1
diff --git a/bio/gatk/applybqsrspark/environment.yaml b/bio/gatk/applybqsrspark/environment.yaml
@@ -4,5 +4,5 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
   - samtools =1.16.1
diff --git a/bio/gatk/applyvqsr/environment.yaml b/bio/gatk/applyvqsr/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/applyvqsr/test/Snakefile b/bio/gatk/applyvqsr/test/Snakefile
@@ -12,6 +12,6 @@ rule apply_vqsr:
         mode="SNP",  # set mode, must be either SNP, INDEL or BOTH
         extra="",  # optional
     resources:
-        mem_mb=50,
+        mem_mb=1024,
     wrapper:
         "master/bio/gatk/applyvqsr"
diff --git a/bio/gatk/baserecalibrator/environment.yaml b/bio/gatk/baserecalibrator/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/baserecalibratorspark/environment.yaml b/bio/gatk/baserecalibratorspark/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/cleansam/environment.yaml b/bio/gatk/cleansam/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/combinegvcfs/environment.yaml b/bio/gatk/combinegvcfs/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/depthofcoverage/environment.yaml b/bio/gatk/depthofcoverage/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/estimatelibrarycomplexity/environment.yaml b/bio/gatk/estimatelibrarycomplexity/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/filtermutectcalls/environment.yaml b/bio/gatk/filtermutectcalls/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/genomicsdbimport/environment.yaml b/bio/gatk/genomicsdbimport/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.2
-  - snakemake-wrapper-utils =0.5
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/genomicsdbimport/test/Snakefile b/bio/gatk/genomicsdbimport/test/Snakefile
@@ -11,6 +11,6 @@ rule genomics_db_import:
         extra="",  # optional
         java_opts="",  # optional
     resources:
-        mem_mb=1024,
+        mem_mb=lambda wildcards, input: max([input.size_mb * 1.6, 200]),
     wrapper:
         "master/bio/gatk/genomicsdbimport"
diff --git a/bio/gatk/genomicsdbimport/wrapper.py b/bio/gatk/genomicsdbimport/wrapper.py
@@ -10,7 +10,10 @@
 
 
 extra = snakemake.params.get("extra", "")
-java_opts = get_java_opts(snakemake)
+# uses Java native library TileDB, which requires a lot of memory outside
+# of the `-Xmx` memory, so we reserve 40% instead of the default 20%. See:
+# https://gatk.broadinstitute.org/hc/en-us/articles/9570326648475-GenomicsDBImportGenomicsDBImport
+java_opts = get_java_opts(snakemake, java_mem_overhead_factor=0.4)
 
 gvcfs = list(map("--variant {}".format, snakemake.input.gvcfs))
 

diff --git a/bio/gatk/genotypegvcfs/environment.yaml b/bio/gatk/genotypegvcfs/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/getpileupsummaries/environment.yaml b/bio/gatk/getpileupsummaries/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/haplotypecaller/environment.yaml b/bio/gatk/haplotypecaller/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/intervallisttobed/environment.yaml b/bio/gatk/intervallisttobed/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/learnreadorientationmodel/environment.yaml b/bio/gatk/learnreadorientationmodel/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/leftalignandtrimvariants/environment.yaml b/bio/gatk/leftalignandtrimvariants/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/markduplicatesspark/test/Snakefile b/bio/gatk/markduplicatesspark/test/Snakefile
@@ -13,7 +13,9 @@ rule mark_duplicates_spark:
         #spark_master="",  # optional
         #spark_extra="", # optional
     resources:
-        mem_mb=1024,
+        # Memory needs to be at least 471859200 for Spark, so 589824000 when
+        # accounting for default JVM overhead of 20%. We round round to 650M.
+        mem_mb=lambda wildcards, input: max([input.size_mb * 0.25, 650]),
     threads: 8
     wrapper:
         "master/bio/gatk/markduplicatesspark"
diff --git a/bio/gatk/mutect/environment.yaml b/bio/gatk/mutect/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/printreadsspark/environment.yaml b/bio/gatk/printreadsspark/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/scatterintervalsbyns/environment.yaml b/bio/gatk/scatterintervalsbyns/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/selectvariants/environment.yaml b/bio/gatk/selectvariants/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/splitintervals/environment.yaml b/bio/gatk/splitintervals/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/splitncigarreads/environment.yaml b/bio/gatk/splitncigarreads/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/variantannotator/environment.yaml b/bio/gatk/variantannotator/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/varianteval/environment.yaml b/bio/gatk/varianteval/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/variantfiltration/environment.yaml b/bio/gatk/variantfiltration/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk/variantrecalibrator/environment.yaml b/bio/gatk/variantrecalibrator/environment.yaml
@@ -4,6 +4,6 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
   - google-cloud-sdk
   - google-crc32c
diff --git a/bio/gatk/variantstotable/environment.yaml b/bio/gatk/variantstotable/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - gatk4 =4.3.0.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2
diff --git a/bio/gatk3/baserecalibrator/environment.yaml b/bio/gatk3/baserecalibrator/environment.yaml
@@ -5,4 +5,4 @@ channels:
 dependencies:
   - gatk =3.8
   - python =3.11.0
-  - snakemake-wrapper-utils =0.5.0
+  - snakemake-wrapper-utils =0.5.2