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?

workflow/rules/benchmarking.smk

@@ -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/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/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

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

@@ -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
@@ -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:
@@ -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

@@ -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:

workflow/rules/qc.smk

@@ -9,7 +9,7 @@ rule fastqc:
     resources:
         mem_mb=1024,
     wrapper:
-        "v2.10.0/bio/fastqc"
+        "v7.6.0/bio/fastqc"
 
 
 rule samtools_idxstats:
@@ -21,7 +21,7 @@ rule samtools_idxstats:
     log:
         "logs/samtools/idxstats/{sample}.log",
     wrapper:
-        "v2.3.2/bio/samtools/idxstats"
+        "v9.4.1/bio/samtools/idxstats"
 
 
 rule samtools_stats:

workflow/rules/ref.smk

@@ -11,7 +11,7 @@ rule get_genome:
         chromosome=config["ref"].get("chromosome"),
     cache: "omit-software"
     wrapper:
-        "v7.3.0/bio/reference/ensembl-sequence"
+        "v5.10.0/bio/reference/ensembl-sequence"
 
 
 rule genome_faidx:
@@ -23,7 +23,7 @@ rule genome_faidx:
         "logs/genome-faidx.log",
     cache: "omit-software"
     wrapper:
-        "v2.3.2/bio/samtools/faidx"
+        "v9.4.1/bio/samtools/faidx"
 
 
 rule genome_dict:
@@ -56,7 +56,7 @@ rule get_known_variants:
         chromosome=config["ref"].get("chromosome"),
     cache: "omit-software"
     wrapper:
-        "v7.5.0/bio/reference/ensembl-variation"
+        "v9.4.1/bio/reference/ensembl-variation"
 
 
 rule get_annotation:
@@ -120,7 +120,7 @@ rule bwa_index:
         "logs/bwa_index.log",
     cache: True
     wrapper:
-        "v2.3.2/bio/bwa/index"
+        "v5.10.0/bio/bwa/index"
 
 
 rule get_vep_cache:
@@ -145,7 +145,7 @@ rule get_vep_plugins:
     log:
         "logs/vep/plugins.log",
     wrapper:
-        "v8.0.0/bio/vep/plugins"
+        "v9.0.1/bio/vep/plugins"
 
 
 rule get_pangenome:

workflow/rules/utils.smk

@@ -19,7 +19,7 @@ rule bcf_to_vcf_gz:
     log:
         "logs/bcf-to-vcf/{prefix}.log",
     wrapper:
-        "v2.3.2/bio/bcftools/view"
+        "v9.4.1/bio/bcftools/view"
 
 
 rule bam_index:
@@ -30,7 +30,7 @@ rule bam_index:
     log:
         "logs/bam-index/{prefix}.log",
     wrapper:
-        "v2.3.2/bio/samtools/index"
+        "v9.4.1/bio/samtools/index"
 
 
 rule tabix_txt_tsv:
@@ -44,4 +44,4 @@ rule tabix_txt_tsv:
         get_tabix_params,
     cache: "omit-software"
     wrapper:
-        "v2.3.2/bio/tabix/index"
+        "v9.4.1/bio/tabix/index"