diff --git a/.test/config/config.yml b/.test/config/config.yml index 39cd8fa..c0e4bbc 100644 --- a/.test/config/config.yml +++ b/.test/config/config.yml @@ -29,7 +29,13 @@ mapping: sort_extra: "" star: index: "" - extra: "" + extra: + [ + "--outFilterMultimapNmax 10", + "--outSAMmultNmax 1", + "--outMultimapperOrder Random", + "--alignIntronMax 1", + ] minimap2: index: "" extra: "-ax map-ont" diff --git a/config/config.yml b/config/config.yml index 39cd8fa..c0e4bbc 100644 --- a/config/config.yml +++ b/config/config.yml @@ -29,7 +29,13 @@ mapping: sort_extra: "" star: index: "" - extra: "" + extra: + [ + "--outFilterMultimapNmax 10", + "--outSAMmultNmax 1", + "--outMultimapperOrder Random", + "--alignIntronMax 1", + ] minimap2: index: "" extra: "-ax map-ont" diff --git a/config/schemas/config.schema.yml b/config/schemas/config.schema.yml index 2106db9..331779a 100644 --- a/config/schemas/config.schema.yml +++ b/config/schemas/config.schema.yml @@ -77,8 +77,17 @@ properties: type: string description: additional arguments to STAR index extra: - type: string + type: array + items: + type: string description: additional arguments to STAR align + default: + [ + "--outFilterMultimapNmax 10", + "--outSAMmultNmax 1", + "--outMultimapperOrder Random", + "--alignIntronMax 1", + ] minimap2: type: object properties: diff --git a/workflow/rules/bcftools.smk b/workflow/rules/bcftools.smk index 4f36929..4e60193 100644 --- a/workflow/rules/bcftools.smk +++ b/workflow/rules/bcftools.smk @@ -13,7 +13,7 @@ rule bcftools_pileup: log: "results/bcftools/pileup/{sample}.log", wrapper: - "v7.0.0/bio/bcftools/mpileup" + "v9.4.1/bio/bcftools/mpileup" rule bcftools_call: @@ -30,7 +30,7 @@ rule bcftools_call: log: "results/bcftools/call/{sample}.log", wrapper: - "v7.0.0/bio/bcftools/call" + "v9.4.1/bio/bcftools/call" rule bcftools_view: @@ -45,7 +45,7 @@ rule bcftools_view: params: extra=config["variant_calling"]["bcftools_view"]["extra"], wrapper: - "v7.0.0/bio/bcftools/view" + "v9.4.1/bio/bcftools/view" rule bcftools_filter: @@ -61,7 +61,7 @@ rule bcftools_filter: filter=config["variant_calling"]["bcftools_filter"]["filter"], extra=config["variant_calling"]["bcftools_filter"]["extra"], wrapper: - "v7.0.0/bio/bcftools/filter" + "v9.4.1/bio/bcftools/filter" rule bcftools_stats: @@ -74,4 +74,4 @@ rule bcftools_stats: log: "results/{caller}/call/{sample}_stats.log", wrapper: - "v7.0.0/bio/bcftools/stats" + "v9.4.1/bio/bcftools/stats" diff --git a/workflow/rules/bowtie2.smk b/workflow/rules/bowtie2.smk index 95c50ed..757c4d0 100644 --- a/workflow/rules/bowtie2.smk +++ b/workflow/rules/bowtie2.smk @@ -19,7 +19,7 @@ rule bowtie2_build: extra=config["mapping"]["bowtie2"]["index"], threads: 1 wrapper: - "v7.0.0/bio/bowtie2/build" + "v9.4.1/bio/bowtie2/build" rule bowtie2_align: @@ -39,4 +39,4 @@ rule bowtie2_align: extra=config["mapping"]["bowtie2"]["extra"], threads: 8 wrapper: - "v7.0.0/bio/bowtie2/align" + "v9.4.1/bio/bowtie2/align" diff --git a/workflow/rules/bwamem2.smk b/workflow/rules/bwamem2.smk index c651bba..ab39f26 100644 --- a/workflow/rules/bwamem2.smk +++ b/workflow/rules/bwamem2.smk @@ -15,7 +15,7 @@ rule bwa_mem2_index: message: "build bwa_mem2 index" wrapper: - "v6.2.0/bio/bwa-mem2/index" + "v7.2.0/bio/bwa-mem2/index" rule bwa_mem2: @@ -38,4 +38,4 @@ rule bwa_mem2: sort_extra=config["mapping"]["bwa_mem2"]["sort_extra"], threads: 8 wrapper: - "v6.2.0/bio/bwa-mem2/mem" + "v9.4.1/bio/bwa-mem2/mem" diff --git a/workflow/rules/freebayes.smk b/workflow/rules/freebayes.smk index 6bb3faf..1d7acde 100644 --- a/workflow/rules/freebayes.smk +++ b/workflow/rules/freebayes.smk @@ -14,4 +14,4 @@ rule freebayes: "call variants using freebayes" threads: 4 wrapper: - "v7.0.0/bio/freebayes" + "v9.4.1/bio/freebayes" diff --git a/workflow/rules/mapping_stats.smk b/workflow/rules/mapping_stats.smk index 979b18b..967280f 100644 --- a/workflow/rules/mapping_stats.smk +++ b/workflow/rules/mapping_stats.smk @@ -11,7 +11,7 @@ rule samtools_sort: extra=config["mapping"]["samtools_sort"]["extra"], threads: 2 wrapper: - "v7.0.0/bio/samtools/sort" + "v9.4.1/bio/samtools/sort" rule samtools_index: @@ -27,7 +27,7 @@ rule samtools_index: extra=config["mapping"]["samtools_index"]["extra"], threads: 2 wrapper: - "v7.0.0/bio/samtools/index" + "v9.4.1/bio/samtools/index" rule gffread_gff: @@ -44,7 +44,7 @@ rule gffread_gff: params: extra=config["mapping_stats"]["gffread"]["extra"], wrapper: - "v7.0.0/bio/gffread" + "v5.0.0/bio/gffread" rule rseqc_infer_experiment: @@ -60,7 +60,7 @@ rule rseqc_infer_experiment: params: extra="--sample-size 10000", wrapper: - "v7.0.0/bio/rseqc/infer_experiment" + "v4.7.5/bio/rseqc/infer_experiment" rule rseqc_bam_stat: @@ -76,7 +76,7 @@ rule rseqc_bam_stat: message: "collect mapping statistics using RSeQC" wrapper: - "v7.0.0/bio/rseqc/bam_stat" + "v5.0.0/bio/rseqc/bam_stat" rule deeptools_coverage: @@ -96,4 +96,4 @@ rule deeptools_coverage: message: "generate normalized coverage files using deeptools" wrapper: - "v7.0.0/bio/deeptools/bamcoverage" + "v5.6.0/bio/deeptools/bamcoverage" diff --git a/workflow/rules/minimap2.smk b/workflow/rules/minimap2.smk index 1f07390..ca17957 100644 --- a/workflow/rules/minimap2.smk +++ b/workflow/rules/minimap2.smk @@ -9,7 +9,7 @@ rule minimap2_index: extra=config["mapping"]["minimap2"]["index"], threads: 1 wrapper: - "v7.2.0/bio/minimap2/index" + "v7.1.0/bio/minimap2/index" rule minimap2_align: @@ -29,4 +29,4 @@ rule minimap2_align: sort_extra=config["mapping"]["minimap2"]["sort_extra"], threads: 8 wrapper: - "v7.2.0/bio/minimap2/aligner" + "v9.4.1/bio/minimap2/aligner" diff --git a/workflow/rules/process_reads.smk b/workflow/rules/process_reads.smk index 1e9cb68..587db84 100644 --- a/workflow/rules/process_reads.smk +++ b/workflow/rules/process_reads.smk @@ -62,4 +62,4 @@ rule fastp: resources: mem_mb=4096, wrapper: - "v7.0.0/bio/fastp" + "v9.4.1/bio/fastp" diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk index 41ce076..1253125 100644 --- a/workflow/rules/qc.smk +++ b/workflow/rules/qc.smk @@ -14,7 +14,7 @@ rule fastqc: resources: mem_mb=4096, wrapper: - "v6.0.0/bio/fastqc" + "v7.6.0/bio/fastqc" rule multiqc: @@ -29,4 +29,4 @@ rule multiqc: log: "results/multiqc/multiqc.log", wrapper: - "v6.0.0/bio/multiqc" + "v8.1.1/bio/multiqc" diff --git a/workflow/rules/report.smk b/workflow/rules/report.smk index 1f6d9ea..60a685d 100644 --- a/workflow/rules/report.smk +++ b/workflow/rules/report.smk @@ -11,7 +11,7 @@ rule bcftools_bcf_and_index: params: extra="--write-index", wrapper: - "v7.2.0/bio/bcftools/view" + "v9.4.1/bio/bcftools/view" rule bcftools_intersection: diff --git a/workflow/rules/star.smk b/workflow/rules/star.smk index e7c498b..6456f36 100644 --- a/workflow/rules/star.smk +++ b/workflow/rules/star.smk @@ -11,7 +11,7 @@ rule star_index: message: "build star index" wrapper: - "v7.2.0/bio/star/index" + "v3.3.7/bio/star/index" rule star_align: @@ -30,4 +30,4 @@ rule star_align: extra=config["mapping"]["star"]["extra"], threads: 8 wrapper: - "v7.2.0/bio/star/align" + "v3.3.7/bio/star/align" diff --git a/workflow/rules/variant_annotation.smk b/workflow/rules/variant_annotation.smk index 2fce545..773edf0 100644 --- a/workflow/rules/variant_annotation.smk +++ b/workflow/rules/variant_annotation.smk @@ -26,7 +26,7 @@ rule vep_plugins: log: "results/vep/plugins.log", wrapper: - "v7.2.0/bio/vep/plugins" + "v9.0.1/bio/vep/plugins" rule vep_annotate_variants: @@ -49,7 +49,7 @@ rule vep_annotate_variants: "annotate variants using VEP" threads: 4 wrapper: - "v7.2.0/bio/vep/annotate" + "v9.4.0/bio/vep/annotate" rule snpeff_prepare: