Merge pull request #7 from TRON-Bioinformatics/fix-vafator-params

remove cleanup + refactor modules parameters

Author: priesgo

main.nf

@@ -18,12 +18,8 @@ params.skip_decompose_complex = false
 params.filter = false
 params.cpus = 1
 params.memory = "4g"
-params.vcf_without_ad = false
-params.mapping_quality = 0
-params.base_call_quality = 0
 params.skip_multiallelic_filter = false
 params.snpeff_organism = false
-params.snpeff_args = ""
 params.snpeff_datadir = false
 
 

modules/04_vafator.nf

@@ -3,7 +3,6 @@ params.memory = "4g"
 params.output = ""
 params.mapping_quality = 0
 params.base_call_quality = 0
-params.skip_multiallelic_filter = false
 params.enable_conda = false
 
 
@@ -27,9 +26,9 @@ process VAFATOR {
     vafator \
     --input-vcf ${vcf} \
     --output-vcf ${vcf.baseName}.vaf.vcf \
-    ${bams_param} \
     --mapping-quality ${params.mapping_quality} \
-    --base-call-quality ${params.base_call_quality}
+    --base-call-quality ${params.base_call_quality} \
+    ${bams_param}
     """
 }
 

nextflow.config

@@ -27,9 +27,7 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-VERSION = '2.1.3'
-
-cleanup=true
+VERSION = '2.1.4'
 
 manifest {
   name = 'TRON-Bioinformatics/tronflow-vcf-postprocessing'