perf: autobump snakemake wrappers

Author: johanneskoester

workflow/rules/annotation.smk

@@ -21,7 +21,7 @@ rule annotate_candidate_variants:
     group:
         "candidate-annotation"
     wrapper:
-        "v8.0.0/bio/vep/annotate"
+        "v9.4.0/bio/vep/annotate"
 
 
 rule annotate_variants:
@@ -63,7 +63,7 @@ rule annotate_variants:
     group:
         "annotation"
     wrapper:
-        "v8.0.0/bio/vep/annotate"
+        "v9.4.0/bio/vep/annotate"
 
 
 # TODO What about multiple ID Fields?
@@ -128,4 +128,4 @@ rule gather_annotated_calls:
     group:
         "annotation"
     wrapper:
-        "v2.3.2/bio/bcftools/concat"
+        "v9.4.2/bio/bcftools/concat"

workflow/rules/benchmarking.smk

@@ -13,7 +13,7 @@ rule gather_benchmark_calls:
     params:
         extra="-a",
     wrapper:
-        "v2.3.2/bio/bcftools/concat"
+        "v9.4.2/bio/bcftools/concat"
 
 
 rule chm_eval_sample:
@@ -23,7 +23,7 @@ rule chm_eval_sample:
         "logs/benchmarking/chm-eval-sample.log",
     cache: "omit-software"
     wrapper:
-        "v2.3.2/bio/benchmark/chm-eval-sample"
+        "v9.4.2/bio/benchmark/chm-eval-sample"
 
 
 rule chm_namesort:
@@ -37,7 +37,7 @@ rule chm_namesort:
     resources:
         mem_mb=64000,
     wrapper:
-        "v8.1.1/bio/samtools/sort"
+        "v9.4.2/bio/samtools/sort"
 
 
 rule chm_to_fastq:
@@ -65,7 +65,7 @@ rule chm_eval_kit:
         "logs/benchmarking/chm-eval-kit.log",
     cache: True
     wrapper:
-        "v2.3.2/bio/benchmark/chm-eval-kit"
+        "v2.9.1/bio/benchmark/chm-eval-kit"
 
 
 rule chromosome_map:
@@ -111,4 +111,4 @@ rule chm_eval:
     log:
         "logs/benchmarking/{query}.chm-eval.log",
     wrapper:
-        "v2.3.2/bio/benchmark/chm-eval"
+        "v2.9.1/bio/benchmark/chm-eval"

workflow/rules/calling.smk

@@ -110,7 +110,7 @@ rule sort_calls:
     resources:
         mem_mb=8000,
     wrapper:
-        "v2.6.0/bio/bcftools/sort"
+        "v9.4.2/bio/bcftools/sort"
 
 
 rule bcftools_concat:
@@ -124,4 +124,4 @@ rule bcftools_concat:
     params:
         extra="-a",  # TODO Check this
     wrapper:
-        "v2.3.2/bio/bcftools/concat"
+        "v9.4.2/bio/bcftools/concat"

workflow/rules/candidate_calling.smk

@@ -20,7 +20,7 @@ rule freebayes:
         ),
     threads: 96  # with more cores, we expect freebayes to become too IO bound and memory hungry
     wrapper:
-        "v2.7.0/bio/freebayes"
+        "v9.4.2/bio/freebayes"
 
 
 rule delly:
@@ -38,7 +38,7 @@ rule delly:
         extra=config["params"].get("delly", ""),
     threads: lambda _, input: len(input.alns)  # delly parallelizes over the number of samples
     wrapper:
-        "v2.3.2/bio/delly"
+        "v9.4.2/bio/delly"
 
 
 # Delly breakends lead to invalid BCFs after VEP annotation (invalid RLEN). Therefore we exclude them for now.
@@ -67,7 +67,7 @@ rule filter_offtarget_variants:
     log:
         "logs/filter_offtarget_variants/{group}/{group}.{caller}.log",
     wrapper:
-        "v2.3.2/bio/bcftools/filter"
+        "v9.4.2/bio/bcftools/filter"
 
 
 rule scatter_candidates:

workflow/rules/datavzrd.smk

@@ -111,7 +111,7 @@ rule datavzrd_variants_calls:
             dpath="calling/fdr-control/events/{event}/desc", within=config
         ),
     wrapper:
-        "v9.2.0/utils/datavzrd"
+        "v9.4.1/utils/datavzrd"
 
 
 rule datavzrd_fusion_calls:
@@ -150,7 +150,7 @@ rule datavzrd_fusion_calls:
         species=lookup(within=config, dpath="ref/species"),
         samples=samples,
     wrapper:
-        "v9.2.0/utils/datavzrd"
+        "v9.4.1/utils/datavzrd"
 
 
 rule bedtools_merge:
@@ -165,7 +165,7 @@ rule bedtools_merge:
     log:
         "logs/bedtools/{group}/{sample}.log",
     wrapper:
-        "v2.6.0/bio/bedtools/intersect"
+        "v9.4.1/bio/bedtools/intersect"
 
 
 rule coverage_table:
@@ -204,4 +204,4 @@ rule datavzrd_coverage:
     params:
         samples=lambda wc: get_group_samples(wc.group),
     wrapper:
-        "v9.2.0/utils/datavzrd"
+        "v9.4.1/utils/datavzrd"

workflow/rules/filtering.smk

@@ -62,7 +62,7 @@ rule gather_calls:
     params:
         extra="-a",
     wrapper:
-        "v2.3.2/bio/bcftools/concat"
+        "v9.4.2/bio/bcftools/concat"
 
 
 rule control_fdr:
@@ -92,7 +92,7 @@ rule merge_calls:
     params:
         extra="-a",
     wrapper:
-        "v2.3.2/bio/bcftools/concat"
+        "v9.4.2/bio/bcftools/concat"
 
 
 rule convert_phred_scores:

workflow/rules/fusion_calling.smk

@@ -1,6 +1,6 @@
 module fusion_calling:
     meta_wrapper:
-        "v8.0.0/meta/bio/star_arriba"
+        "v9.0.1/meta/bio/star_arriba"
     pathvars:
         results="results",  # Path to results directory
         resources="resources",  # Path to resources directory
@@ -95,7 +95,7 @@ rule sort_arriba_calls:
     resources:
         mem_mb=8000,
     wrapper:
-        "v1.21.0/bio/bcftools/sort"
+        "v9.4.2/bio/bcftools/sort"
 
 
 rule bcftools_concat_candidates:
@@ -113,4 +113,4 @@ rule bcftools_concat_candidates:
     resources:
         mem_mb=10,
     wrapper:
-        "v1.21.0/bio/bcftools/concat"
+        "v9.4.2/bio/bcftools/concat"

workflow/rules/maf.smk

@@ -6,7 +6,7 @@ rule group_bcf_to_vcf:
     log:
         "logs/maf/{group}/{group}.{event}.{calling_type}.fdr-controlled.log",
     wrapper:
-        "v3.8.0/bio/bcftools/view"
+        "v9.4.1/bio/bcftools/view"
 
 
 rule group_vcf_to_maf:

workflow/rules/mapping.smk

@@ -10,7 +10,7 @@ rule map_reads_bwa:
         extra=get_read_group("-R "),
     threads: 8
     wrapper:
-        "v3.8.0/bio/bwa/mem"
+        "v9.4.2/bio/bwa/mem"
 
 
 rule count_sample_kmers:
@@ -74,7 +74,7 @@ rule map_reads_vg:
         sorting="none",
     threads: 64
     wrapper:
-        "v6.1.0/bio/vg/giraffe"
+        "v9.4.2/bio/vg/giraffe"
 
 
 rule reheader_mapped_reads:
@@ -105,7 +105,7 @@ rule fix_mate:
     params:
         extra="",
     wrapper:
-        "v4.7.2/bio/samtools/fixmate"
+        "v9.4.1/bio/samtools/fixmate"
 
 
 # adding read groups is exclusive to vg mapped reads and
@@ -146,7 +146,7 @@ rule sort_alignments:
     resources:
         mem_mb=32000,
     wrapper:
-        "v8.1.1/bio/samtools/sort"
+        "v9.4.2/bio/samtools/sort"
 
 
 rule annotate_umis:
@@ -177,7 +177,7 @@ rule mark_duplicates:
         #https://broadinstitute.github.io/picard/faq.html
         mem_mb=3000,
     wrapper:
-        "v2.5.0/bio/picard/markduplicates"
+        "v9.4.2/bio/picard/markduplicates"
 
 
 rule calc_consensus_reads:
@@ -213,7 +213,7 @@ rule map_consensus_reads:
         "logs/bwa_mem/{sample}.{read_type}.consensus.log",
     threads: 8
     wrapper:
-        "v2.3.2/bio/bwa/mem"
+        "v9.4.2/bio/bwa/mem"
 
 
 rule merge_consensus_reads:
@@ -227,7 +227,7 @@ rule merge_consensus_reads:
         "logs/samtools_merge/{sample}.log",
     threads: 8
     wrapper:
-        "v2.3.2/bio/samtools/merge"
+        "v9.4.1/bio/samtools/merge"
 
 
 rule sort_consensus_reads:
@@ -241,7 +241,7 @@ rule sort_consensus_reads:
     resources:
         mem_mb=64000,
     wrapper:
-        "v8.1.1/bio/samtools/sort"
+        "v9.4.2/bio/samtools/sort"
 
 
 # TODO Does not use consensus reads
@@ -263,7 +263,7 @@ rule splitncigarreads:
     resources:
         mem_mb=1024,
     wrapper:
-        "v3.1.0/bio/gatk/splitncigarreads"
+        "v7.6.0/bio/gatk/splitncigarreads"
 
 
 rule recalibrate_base_qualities:
@@ -286,7 +286,7 @@ rule recalibrate_base_qualities:
         "logs/gatk/baserecalibrator/{sample}.log",
     threads: 8
     wrapper:
-        "v1.25.0/bio/gatk/baserecalibratorspark"
+        "v7.6.0/bio/gatk/baserecalibratorspark"
 
 
 ruleorder: apply_bqsr > bam_index
@@ -309,4 +309,4 @@ rule apply_bqsr:
         extra=config["params"]["gatk"]["applyBQSR"],  # optional
         java_opts="",  # optional
     wrapper:
-        "v2.3.2/bio/gatk/applybqsr"
+        "v9.4.1/bio/gatk/applybqsr"

workflow/rules/primers.smk

@@ -59,7 +59,7 @@ rule map_primers:
         sort_extra="",  # Extra args for samtools/picard.
     threads: 8
     wrapper:
-        "v2.13.0/bio/bwa/mem"
+        "v9.4.2/bio/bwa/mem"
 
 
 rule filter_unmapped_primers:
@@ -72,7 +72,7 @@ rule filter_unmapped_primers:
     log:
         "logs/primers/{panel}_primers_filtered.log",
     wrapper:
-        "v2.3.2/bio/samtools/view"
+        "v9.4.1/bio/samtools/view"
 
 
 rule primer_to_bed: