perf: update all wrappers to latest wrapper versions with changes

workflow/rules/annotation.smk

@@ -21,7 +21,7 @@ rule annotate_candidate_variants:
     group:
         "candidate-annotation"
     wrapper:
-        "v3.3.5/bio/vep/annotate"
+        "v7.6.0/bio/vep/annotate"
 
 
 rule annotate_variants:
@@ -49,7 +49,7 @@ rule annotate_variants:
     group:
         "annotation"
     wrapper:
-        "v3.3.5/bio/vep/annotate"
+        "v7.6.0/bio/vep/annotate"
 
 
 # TODO What about multiple ID Fields?
@@ -114,4 +114,4 @@ rule gather_annotated_calls:
     group:
         "annotation"
     wrapper:
-        "v2.3.2/bio/bcftools/concat"
+        "v7.6.0/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"
+        "v7.6.0/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"
+        "v7.3.0/bio/benchmark/chm-eval-sample"
 
 
 rule chm_namesort:
@@ -37,7 +37,7 @@ rule chm_namesort:
         "logs/benchmarking/samtools-namesort.log",
     threads: workflow.cores - 1
     wrapper:
-        "v2.3.2/bio/samtools/sort"
+        "v7.6.0/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

@@ -108,7 +108,7 @@ rule sort_calls:
     resources:
         mem_mb=8000,
     wrapper:
-        "v2.6.0/bio/bcftools/sort"
+        "v7.6.0/bio/bcftools/sort"
 
 
 rule bcftools_concat:
@@ -122,4 +122,4 @@ rule bcftools_concat:
     params:
         extra="-a",  # TODO Check this
     wrapper:
-        "v2.3.2/bio/bcftools/concat"
+        "v7.6.0/bio/bcftools/concat"

workflow/rules/candidate_calling.smk

@@ -20,7 +20,7 @@ rule freebayes:
         ),
     threads: max(workflow.cores - 1, 1)  # use all available cores -1 (because of the pipe) for calling
     wrapper:
-        "v2.7.0/bio/freebayes"
+        "v7.6.0/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"
+        "v7.6.0/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}.{caller}.log",
     wrapper:
-        "v2.3.2/bio/bcftools/filter"
+        "v7.6.0/bio/bcftools/filter"
 
 
 rule scatter_candidates:

workflow/rules/datavzrd.smk

@@ -103,7 +103,7 @@ rule datavzrd_variants_calls:
             dpath="calling/fdr-control/events/{event}/desc", within=config
         ),
     wrapper:
-        "v6.2.0/utils/datavzrd"
+        "v7.6.0/utils/datavzrd"
 
 
 rule datavzrd_fusion_calls:
@@ -141,7 +141,7 @@ rule datavzrd_fusion_calls:
         groups=get_report_batch("fusions"),
         samples=samples,
     wrapper:
-        "v6.2.0/utils/datavzrd"
+        "v7.6.0/utils/datavzrd"
 
 
 rule bedtools_merge:
@@ -156,7 +156,7 @@ rule bedtools_merge:
     log:
         "logs/bedtools/{group}/{sample}.log",
     wrapper:
-        "v2.6.0/bio/bedtools/intersect"
+        "v7.3.0/bio/bedtools/intersect"
 
 
 rule coverage_table:
@@ -195,4 +195,4 @@ rule datavzrd_coverage:
     params:
         samples=lambda wc: get_group_samples(wc.group),
     wrapper:
-        "v6.2.0/utils/datavzrd"
+        "v7.6.0/utils/datavzrd"

workflow/rules/filtering.smk

@@ -62,7 +62,7 @@ rule gather_calls:
     params:
         extra="-a",
     wrapper:
-        "v2.3.2/bio/bcftools/concat"
+        "v7.6.0/bio/bcftools/concat"
 
 
 rule control_fdr:
@@ -92,7 +92,7 @@ rule merge_calls:
     params:
         extra="-a",
     wrapper:
-        "v2.3.2/bio/bcftools/concat"
+        "v7.6.0/bio/bcftools/concat"
 
 
 rule convert_phred_scores:

workflow/rules/fusion_calling.smk

@@ -1,6 +1,6 @@
 module fusion_calling:
     meta_wrapper:
-        "v7.1.0/meta/bio/star_arriba"
+        "v1.26.0/meta/bio/star_arriba"
     config:
         config
 
@@ -95,7 +95,7 @@ rule sort_arriba_calls:
     resources:
         mem_mb=8000,
     wrapper:
-        "v1.21.0/bio/bcftools/sort"
+        "v7.6.0/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"
+        "v7.6.0/bio/bcftools/concat"

workflow/rules/maf.smk

@@ -6,7 +6,7 @@ rule group_bcf_to_vcf:
     log:
         "logs/maf/{group}.{event}.{calling_type}.fdr-controlled.log",
     wrapper:
-        "v3.8.0/bio/bcftools/view"
+        "v7.6.0/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"
+        "v7.6.0/bio/bwa/mem"
 
 
 rule count_sample_kmers:
@@ -73,7 +73,7 @@ rule map_reads_vg:
         sorting="none",
     threads: 64
     wrapper:
-        "v6.1.0/bio/vg/giraffe"
+        "v7.6.0/bio/vg/giraffe"
 
 
 rule reheader_mapped_reads:
@@ -104,7 +104,7 @@ rule fix_mate:
     params:
         extra="",
     wrapper:
-        "v4.7.2/bio/samtools/fixmate"
+        "v7.6.0/bio/samtools/fixmate"
 
 
 # adding read groups is exclusive to vg mapped reads and
@@ -147,7 +147,7 @@ rule sort_alignments:
     resources:
         mem="8GB",
     wrapper:
-        "v5.10.0/bio/samtools/sort"
+        "v7.6.0/bio/samtools/sort"
 
 
 rule annotate_umis:
@@ -178,7 +178,7 @@ rule mark_duplicates:
         #https://broadinstitute.github.io/picard/faq.html
         mem_mb=3000,
     wrapper:
-        "v2.5.0/bio/picard/markduplicates"
+        "v7.6.0/bio/picard/markduplicates"
 
 
 rule calc_consensus_reads:
@@ -214,7 +214,7 @@ rule map_consensus_reads:
         "logs/bwa_mem/{sample}.{read_type}.consensus.log",
     threads: 8
     wrapper:
-        "v2.3.2/bio/bwa/mem"
+        "v7.6.0/bio/bwa/mem"
 
 
 rule merge_consensus_reads:
@@ -228,7 +228,7 @@ rule merge_consensus_reads:
         "logs/samtools_merge/{sample}.log",
     threads: 8
     wrapper:
-        "v2.3.2/bio/samtools/merge"
+        "v7.6.0/bio/samtools/merge"
 
 
 rule sort_consensus_reads:
@@ -240,7 +240,7 @@ rule sort_consensus_reads:
         "logs/samtools_sort/{sample}.log",
     threads: 16
     wrapper:
-        "v2.3.2/bio/samtools/sort"
+        "v7.6.0/bio/samtools/sort"
 
 
 # TODO Does not use consensus reads
@@ -262,7 +262,7 @@ rule splitncigarreads:
     resources:
         mem_mb=1024,
     wrapper:
-        "v3.1.0/bio/gatk/splitncigarreads"
+        "v7.6.0/bio/gatk/splitncigarreads"
 
 
 rule recalibrate_base_qualities:
@@ -285,7 +285,7 @@ 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
@@ -308,4 +308,4 @@ rule apply_bqsr:
         extra=config["params"]["gatk"]["applyBQSR"],  # optional
         java_opts="",  # optional
     wrapper:
-        "v2.3.2/bio/gatk/applybqsr"
+        "v7.6.0/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"
+        "v7.6.0/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"
+        "v7.6.0/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"
+        "v7.6.0/bio/samtools/idxstats"
 
 
 rule samtools_stats:
@@ -32,7 +32,7 @@ rule samtools_stats:
     log:
         "logs/samtools/stats/{sample}.log",
     wrapper:
-        "v2.3.2/bio/samtools/stats"
+        "v7.6.0/bio/samtools/stats"
 
 
 rule multiqc:
@@ -50,4 +50,4 @@ rule multiqc:
     log:
         "logs/multiqc/{group}.log",
     wrapper:
-        "v2.10.0/bio/multiqc"
+        "v7.6.0/bio/multiqc"

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"
+        "v7.6.0/bio/samtools/faidx"
 
 
 rule genome_dict:
@@ -71,7 +71,7 @@ rule get_annotation:
         "logs/get_annotation.log",
     cache: "omit-software"  # save space and time with between workflow caching (see docs)
     wrapper:
-        "v7.5.0/bio/reference/ensembl-annotation"
+        "v7.4.0/bio/reference/ensembl-annotation"
 
 
 rule determine_coding_regions:
@@ -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:
@@ -134,7 +134,7 @@ rule get_vep_cache:
         "logs/vep/cache.log",
     cache: "omit-software"
     wrapper:
-        "v7.5.0/bio/vep/cache"
+        "v7.6.0/bio/vep/cache"
 
 
 rule get_vep_plugins:

workflow/rules/regions.smk

@@ -46,7 +46,7 @@ rule build_sample_regions:
         extra="--no-per-base",
         quantize="1:",
     wrapper:
-        "v2.3.2/bio/mosdepth"
+        "v7.3.0/bio/mosdepth"
 
 
 rule merge_expanded_group_regions: