perf: update snakemake wrappers to 7.0.0

workflow/rules/download.smk

@@ -76,7 +76,7 @@ rule normalize_truth:
     log:
         "logs/normalize-truth/{genome}.log",
     wrapper:
-        "v1.9.0/bio/bcftools/norm"
+        "v7.0.0/bio/bcftools/norm"
 
 
 rule get_confidence_bed:
@@ -149,8 +149,9 @@ rule get_reference:
         chromosome="1" if config.get("limit-reads") else None,
     log:
         "logs/get-genome.log",
+    cache: "omit-software"  # save space and time with between workflow caching (see docs)
     wrapper:
-        "v1.7.2/bio/reference/ensembl-sequence"
+        "v7.0.0/bio/reference/ensembl-sequence"
 
 
 rule get_liftover_chain:
@@ -172,7 +173,7 @@ rule samtools_faidx:
     log:
         "logs/samtools-faidx.log",
     wrapper:
-        "v6.2.0/bio/samtools/faidx"
+        "v7.0.0/bio/samtools/faidx"
 
 
 rule bwa_index:
@@ -183,9 +184,9 @@ rule bwa_index:
             "resources/reference/genome", ".amb", ".ann", ".bwt", ".pac", ".sa"
         ),
     log:
-        "logs/bwa-index.log",
+        "logs/bwa_index/genome.log",
     wrapper:
-        "v1.8.0/bio/bwa/index"
+        "v7.0.0/bio/bwa/index"
 
 
 rule bwa_mem:
@@ -197,11 +198,12 @@ rule bwa_mem:
     log:
         "logs/bwa-mem/{benchmark}.log",
     params:
+        extra=r"-R '@RG\tID:{benchmark}\tSM:{benchmark}'",
         sorting="samtools",  # Can be 'none', 'samtools' or 'picard'.
         sort_order="coordinate",  # Can be 'queryname' or 'coordinate'.
     threads: 8
     wrapper:
-        "v1.8.0/bio/bwa/mem"
+        "v7.0.0/bio/bwa/mem"
 
 
 rule mark_duplicates:
@@ -217,7 +219,7 @@ rule mark_duplicates:
     resources:
         mem_mb=1024,
     wrapper:
-        "v1.7.2/bio/picard/markduplicates"
+        "v7.0.0/bio/picard/markduplicates"
 
 
 rule samtools_index:
@@ -227,8 +229,9 @@ rule samtools_index:
         "results/read-alignments/{benchmark}.dedup.bam.bai",
     log:
         "logs/samtools-index/{benchmark}.log",
+    threads: 4  # This value - 1 will be sent to -@
     wrapper:
-        "v1.7.2/bio/samtools/index"
+        "v7.0.0/bio/samtools/index"
 
 
 rule mosdepth:
@@ -244,8 +247,10 @@ rule mosdepth:
     params:
         extra="--no-per-base --mapq 59",  # we do not want low MAPQ regions end up being marked as high coverage
         quantize=get_mosdepth_quantize,
+    # additional decompression threads through `--threads`
+    threads: 4  # This value - 1 will be sent to `--threads`
     wrapper:
-        "v1.7.2/bio/mosdepth"
+        "v7.0.0/bio/mosdepth"
 
 
 rule stratify_regions:

workflow/rules/eval.smk

@@ -106,7 +106,7 @@ rule remove_non_pass:
     params:
         extra="-f 'PASS,.'",
     wrapper:
-        "v3.3.6/bio/bcftools/view"
+        "v7.0.0/bio/bcftools/view"
 
 
 rule intersect_calls_with_target_regions:
@@ -202,7 +202,7 @@ rule index_stratified_truth:
     log:
         "logs/bcftools-index/{benchmark}.truth.{cov}.log",
     wrapper:
-        "v1.7.2/bio/bcftools/index"
+        "v7.0.0/bio/bcftools/index"
 
 
 checkpoint stat_truth:
@@ -337,7 +337,7 @@ rule report_precision_recall:
         genome=get_genome_name,
         version=get_genome_version,
     wrapper:
-        "v5.0.1/utils/datavzrd"
+        "v7.0.0/utils/datavzrd"
 
 
 rule extract_fp_fn:
@@ -437,7 +437,7 @@ rule report_fp_fn:
         labels=lambda w: get_callsets_labels(get_genome_callsets(w.genome)),
         version=get_genome_version,
     wrapper:
-        "v5.0.1/utils/datavzrd"
+        "v7.0.0/utils/datavzrd"
 
 
 rule report_fp_fn_callset:
@@ -467,4 +467,4 @@ rule report_fp_fn_callset:
         somatic=get_somatic_status,
         high_coverage=get_high_coverage_status,
     wrapper:
-        "v5.0.1/utils/datavzrd"
+        "v7.0.0/utils/datavzrd"

workflow/rules/utils.smk

@@ -6,7 +6,7 @@ rule index_vcf:
     log:
         "logs/bcftools-index-vcf/{prefix}.log",
     wrapper:
-        "v1.9.0/bio/bcftools/index"
+        "v7.0.0/bio/bcftools/index"
 
 
 rule index_bcf:
@@ -17,4 +17,4 @@ rule index_bcf:
     log:
         "logs/bcftools-index-bcf/{prefix}.log",
     wrapper:
-        "v6.2.0/bio/bcftools/index"
+        "v7.0.0/bio/bcftools/index"