fix: added missing star options, bump wrappers

.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"

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"

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:

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"

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"

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"

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"

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"

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"

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"

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"

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:

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"

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: