update help

README.md

@@ -51,6 +51,22 @@ Input:
     sample2	/path/to/your/file2.vcf
 
 Optional input:
+    * --input_bams: a tab-separated values file containing in each row the sample name and path to a BAM file for VAFator annotations
+    The input file does not have header!
+    Example input file:
+    sample1	primary:/path/to/your/file.vcf
+    sample1	metastasis:/path/to/your/file2.vcf
+    * --input_purities: a tab-separated values file containing in each row the sample name and a purity value for VAFator annotations
+    The input file does not have header!
+    Example input file:
+    sample1	primary:0.5
+    sample1	metastasis:0.6
+    * --input_clonalities: a tab-separated values file containing in each row the sample name and a either a 
+    genome-wide clonality value or a Bedgraph file with local clonality values for VAFator annotations
+    The input file does not have header!
+    Example input file:
+    sample1	primary:3
+    sample1	metastasis:/path/to/metastasis.local_clonalities.bed
     * --reference: path to the FASTA genome reference (indexes expected *.fai, *.dict) [required for normalization]
     * --vcf-without-ad: indicate when the VCFs to normalize do not have the FORMAT/AD annotation
     * --output: the folder where to publish output

main.nf

@@ -10,10 +10,10 @@ include { VARIANT_ANNOTATION } from './modules/05_variant_annotation'
 
 params.help= false
 params.input_vcfs = false
+params.input_vcf = false
 
 // optional VAFator inputs
 params.input_bams = false
-params.input_vcf = false
 params.input_purities = false
 params.input_clonalities = false
 

nextflow.config

@@ -55,6 +55,22 @@ Input:
     sample2	/path/to/your/file2.vcf
 
 Optional input:
+    * --input_bams: a tab-separated values file containing in each row the sample name and path to a BAM file for VAFator annotations
+    The input file does not have header!
+    Example input file:
+    sample1	primary:/path/to/your/file.vcf
+    sample1	metastasis:/path/to/your/file2.vcf
+    * --input_purities: a tab-separated values file containing in each row the sample name and a purity value for VAFator annotations
+    The input file does not have header!
+    Example input file:
+    sample1	primary:0.5
+    sample1	metastasis:0.6
+    * --input_clonalities: a tab-separated values file containing in each row the sample name and a either a
+    genome-wide clonality value or a Bedgraph file with local clonality values for VAFator annotations
+    The input file does not have header!
+    Example input file:
+    sample1	primary:3
+    sample1	metastasis:/path/to/metastasis.local_clonalities.bed
     * --reference: path to the FASTA genome reference (indexes expected *.fai, *.dict) [required for normalization]
     * --output: the folder where to publish output
     * --skip_normalization: flag indicating to skip all normalization steps