Merge pull request #6 from TRON-Bioinformatics/fix-vafator-params

ensure VAFator parameters are passed when 0 is provided + change the …

Author: priesgo

README.md

@@ -60,6 +60,8 @@ Optional input:
     * --snpeff_organism: the SnpEff organism name (eg: hg19, hg38, GRCh37.75, GRCh38.99)
     * --snpeff_datadir: the SnpEff data folder where the reference genomes were previously downloaded. Required if --snpeff_organism is provided
     * --snpeff_args: additional SnpEff arguments
+    * --mapping_quality: VAFator minimum mapping quality (default: 0)
+    * --base_call_quality: VAFator minimum base call quality (default: 0)
 
 Output:
     * Normalized VCF file
@@ -206,7 +208,7 @@ chr1	13325	.	CT	C	.	MNV-INDEL	OLD_CLUMPED=chr1:13321:AGCCCT/CGCC	GT:AD:PS	0:229,
 Same as MNVs this behaviour can de disabled with `--skip_decompose_complex`.
 
 
-## Technical annotations
+## Technical annotations (VAFator)
 
 The technical annotations provide an insight on the variant calling process by looking into the context of each variant
 within the pileup of a BAM file. When doing somatic variant calling it may be relevant to have technical annotations

main.nf

@@ -19,8 +19,8 @@ params.filter = false
 params.cpus = 1
 params.memory = "4g"
 params.vcf_without_ad = false
-params.mapping_quality = false
-params.base_call_quality = false
+params.mapping_quality = 0
+params.base_call_quality = 0
 params.skip_multiallelic_filter = false
 params.snpeff_organism = false
 params.snpeff_args = ""

modules/04_vafator.nf

@@ -1,8 +1,8 @@
 params.cpus = 1
 params.memory = "4g"
 params.output = ""
-params.mapping_quality = false
-params.base_call_quality = false
+params.mapping_quality = 0
+params.base_call_quality = 0
 params.skip_multiallelic_filter = false
 params.enable_conda = false
 
@@ -23,12 +23,13 @@ process VAFATOR {
 
     script:
     bams_param = bams.collect { b -> "--bam " + b.split(":").join(" ") }.join(" ")
-    mq_param = params.mapping_quality ? "--mapping-quality " + params.mapping_quality : ""
-    bq_param = params.base_call_quality ? "--base-call-quality " + params.base_call_quality : ""
     """
     vafator \
     --input-vcf ${vcf} \
-    --output-vcf ${vcf.baseName}.vaf.vcf ${bams_param} ${mq_param} ${bq_param}
+    --output-vcf ${vcf.baseName}.vaf.vcf \
+    ${bams_param} \
+    --mapping-quality ${params.mapping_quality} \
+    --base-call-quality ${params.base_call_quality}
     """
 }
 

nextflow.config

@@ -27,7 +27,7 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-VERSION = '2.1.2'
+VERSION = '2.1.3'
 
 cleanup=true
 
@@ -68,6 +68,8 @@ Optional input:
     * --snpeff_organism: the SnpEff organism name (eg: hg19, hg38, GRCh37.75, GRCh38.99)
     * --snpeff_datadir: the SnpEff data folder where the reference genomes were previously downloaded. Required if --snpeff_organism is provided
     * --snpeff_args: additional SnpEff arguments
+    * --mapping_quality: VAFator minimum mapping quality (default: 0)
+    * --base_call_quality: VAFator minimum base call quality (default: 0)
 
 Output:
     * Normalized VCF file