Merge pull request #11 from TRON-Bioinformatics/add-PON-documentation

add missing documentation on PON

README.md

@@ -58,6 +58,7 @@ Optional input:
     * input_normal_bam: comma separated list of normal BAMs (alternative to --input_files)
     * gnomad: path to the gnomad VCF or other germline resource (recommended). If not provided the contamination will 
     not be estimated and the filter of common germline variants will be disabled
+    * pon: path to the panel of normals VCF
     * intervals: path to a BED file containing the regions to analyse
     * output: the folder where to publish output (default: output)
     * enable_bam_output: outputs a new BAM file with the Mutect2 reassembly of reads (default: false)
@@ -161,6 +162,8 @@ The multiple VCFs need to be combined with the GATK tool "CreateSomaticPanelOfNo
 
 This is implemented in the pipeline `mutect2_pon.vcf`.
 
+Once the panel of normals is created pass it to the workflow using the parameter `--pon`.
+
 ### Configuring Funcotator
 
 Funcotator annotation is an optional step. To configure funcotator follow the indications here https://gatk.broadinstitute.org/hc/en-us/articles/360035889931-Funcotator-Information-and-Tutorial.

nextflow.config

@@ -42,7 +42,7 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-VERSION = '1.8.0'
+VERSION = '1.8.1'
 DOI = 'https://zenodo.org/badge/latestdoi/355860788'
 
 manifest {
@@ -78,6 +78,7 @@ Optional input:
     * input_normal_bam: comma separated list of normal BAMs (alternative to --input_files)
     * gnomad: path to the gnomad VCF or other germline resource (recommended). If not provided the contamination will
     not be estimated and the filter of common germline variants will be disabled
+    * pon: path to the panel of normals VCF
     * intervals: path to a BED file containing the regions to analyse
     * output: the folder where to publish output
     * enable_bam_output: outputs a new BAM file with the Mutect2 reassembly of reads (default: false)