Merge pull request #132 from CCBR/varscan-fix

Varscan fix

Author: samarth8392

CHANGELOG.md

@@ -1,5 +1,9 @@
 ## XAVIER development version
 
+## XAVIER 3.1.3
+
+- Fix breaking bug in varscan somaticFilter (#131, @dnousome)
+
 ## XAVIER 3.1.2
 
 - Fix minor bug in `assess_significance.R` script associated with rule `freec_exome_somatic`. (#120, @samarth8392)

CITATION.cff

@@ -46,5 +46,5 @@ identifiers:
   - description: Archived snapshots of all versions
     type: doi
     value: 10.5281/zenodo.12727315
-version: v3.1.2
+version: v3.1.3
 date-released: "2024-11-05"

VERSION

@@ -1 +1 @@
-3.1.2-dev
+3.1.3-dev

config/templates/tools.json

@@ -35,6 +35,7 @@
         "varscan": {
             "version": "2.4.6",
             "filter_settings": "--strand-filter 1 --min-reads2 5 --min-strands2 2 --min-var-freq 0.05 --p-value 0.01 --min-avg-qual 30",
+            "somatic_filter_settings": "--min-reads2 5 --min-strands2 2 --min-var-freq 0.05 --p-value 0.01",
             "modname": "varscan/2.4.6"
         },
         "vcftools": {
@@ -59,7 +60,7 @@
         },
         "sequenza-utils": {
             "version": "3.0.0",
-            "modname": "bedtools/2.30.0"
+            "modname": "sequenza/3.0.0"
         },
         "python": {
             "version": "2.7",

workflow/rules/somatic_snps.paired.smk

@@ -465,7 +465,7 @@ rule varscan_filter:
         genome = config['references']['GENOME'],
         pon = config['references']['PON'],
         basedir = BASEDIR,
-        filter_settings = config['tools']['varscan']['filter_settings'],
+        somatic_filter_settings = config['tools']['varscan']['somatic_filter_settings'],
         ver_varscan = config['tools']['varscan']['version'],
         ver_gatk = config['tools']['gatk4']['version'],
         ver_bcftools = config['tools']['bcftools']['version'],
@@ -484,9 +484,9 @@ rule varscan_filter:
     # mechanism for deletion on exit
     {params.set_tmp}
 
-    varscan filter \\
+    varscan somaticFilter \\
         {input.vcf} \\
-        {params.filter_settings} > {output.filtered1}
+        {params.somatic_filter_settings} --output-file {output.filtered1}
 
     gatk SelectVariants \\
         -R {params.genome} \\