From 161827afd1178dd54c7afc4e173306de9a0d702a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Wed, 11 Jun 2025 13:33:33 +0200 Subject: [PATCH 1/6] chore: update mark_duplicates wrapper to 7.0.0 --- workflow/rules/download.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/download.smk b/workflow/rules/download.smk index 67fb720..30d8d9e 100644 --- a/workflow/rules/download.smk +++ b/workflow/rules/download.smk @@ -217,7 +217,7 @@ rule mark_duplicates: resources: mem_mb=1024, wrapper: - "v1.7.2/bio/picard/markduplicates" + "v7.0.0/bio/picard/markduplicates" rule samtools_index: From d344c8fb9ce1c93ca537ef24ff7baefeb48794da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Thu, 12 Jun 2025 10:40:28 +0200 Subject: [PATCH 2/6] chore: update bwa index and mem --- workflow/rules/download.smk | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/workflow/rules/download.smk b/workflow/rules/download.smk index 30d8d9e..fb1aadb 100644 --- a/workflow/rules/download.smk +++ b/workflow/rules/download.smk @@ -179,13 +179,15 @@ rule bwa_index: input: "resources/reference/genome.fasta", output: - idx=multiext( - "resources/reference/genome", ".amb", ".ann", ".bwt", ".pac", ".sa" + multiext( + "resources/reference/{genome}.{alg}", ".amb", ".ann", ".bwt", ".pac", ".sa" ), log: - "logs/bwa-index.log", + "logs/bwa_index/{genome}.{alg}.log", + params: + extra=lambda w: f"-a {w.alg}", wrapper: - "v1.8.0/bio/bwa/index" + "v7.0.0/bio/bwa/index" rule bwa_mem: @@ -197,11 +199,12 @@ rule bwa_mem: log: "logs/bwa-mem/{benchmark}.log", params: + extra=r"-R '@RG\tID:{sample}\tSM:{sample}'", 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: From e186a157044d83e7633114d4f2c0394db8e1a3d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Thu, 12 Jun 2025 10:41:48 +0200 Subject: [PATCH 3/6] fix: bwa_index output --- workflow/rules/download.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/download.smk b/workflow/rules/download.smk index fb1aadb..0f1adc7 100644 --- a/workflow/rules/download.smk +++ b/workflow/rules/download.smk @@ -179,7 +179,7 @@ rule bwa_index: input: "resources/reference/genome.fasta", output: - multiext( + idx=multiext( "resources/reference/{genome}.{alg}", ".amb", ".ann", ".bwt", ".pac", ".sa" ), log: From 82424d4d5296490931d9fe86e8b689902bb43fae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Thu, 12 Jun 2025 10:45:36 +0200 Subject: [PATCH 4/6] fix: bwa index rule remove wildcards --- workflow/rules/download.smk | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/workflow/rules/download.smk b/workflow/rules/download.smk index 0f1adc7..21d3894 100644 --- a/workflow/rules/download.smk +++ b/workflow/rules/download.smk @@ -180,12 +180,10 @@ rule bwa_index: "resources/reference/genome.fasta", output: idx=multiext( - "resources/reference/{genome}.{alg}", ".amb", ".ann", ".bwt", ".pac", ".sa" + "resources/reference/genome", ".amb", ".ann", ".bwt", ".pac", ".sa" ), log: - "logs/bwa_index/{genome}.{alg}.log", - params: - extra=lambda w: f"-a {w.alg}", + "logs/bwa_index/genome.log", wrapper: "v7.0.0/bio/bwa/index" From ab2660a3cc7337f02bacf4c9738f7fca6f766d2c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Thu, 12 Jun 2025 10:47:26 +0200 Subject: [PATCH 5/6] fix: change from sample to benchmark wildcard bwa mem --- workflow/rules/download.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/download.smk b/workflow/rules/download.smk index 21d3894..597547a 100644 --- a/workflow/rules/download.smk +++ b/workflow/rules/download.smk @@ -197,7 +197,7 @@ rule bwa_mem: log: "logs/bwa-mem/{benchmark}.log", params: - extra=r"-R '@RG\tID:{sample}\tSM:{sample}'", + 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 From 9476183b582bcc2cd86e29599ac32ec7b81cfa2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Thu, 12 Jun 2025 11:12:50 +0200 Subject: [PATCH 6/6] chore: update remaining wrappers to 7.0.0 --- workflow/rules/download.smk | 14 +++++++++----- workflow/rules/eval.smk | 10 +++++----- workflow/rules/utils.smk | 4 ++-- 3 files changed, 16 insertions(+), 12 deletions(-) diff --git a/workflow/rules/download.smk b/workflow/rules/download.smk index 597547a..eaf6b0d 100644 --- a/workflow/rules/download.smk +++ b/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: @@ -228,8 +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: @@ -245,8 +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: diff --git a/workflow/rules/eval.smk b/workflow/rules/eval.smk index 9385639..5304e68 100644 --- a/workflow/rules/eval.smk +++ b/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" diff --git a/workflow/rules/utils.smk b/workflow/rules/utils.smk index 2c76bc1..b0a6480 100644 --- a/workflow/rules/utils.smk +++ b/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"