diff --git a/main.nf b/main.nf index cb574e9..a09e9e2 100755 --- a/main.nf +++ b/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 diff --git a/modules/04_vafator.nf b/modules/04_vafator.nf index a0b4c78..3f3493e 100644 --- a/modules/04_vafator.nf +++ b/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} """ } diff --git a/nextflow.config b/nextflow.config index 439b0f4..957a3cd 100644 --- a/nextflow.config +++ b/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'