Remove bcftools header line

Ensembl · Mar 16, 2023 · 6998e7e · 6998e7e
1 parent e33452e
commit 6998e7e
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/nextflow/nf_modules/merge_VCF.nf b/nextflow/nf_modules/merge_VCF.nf
@@ -46,8 +46,8 @@ process mergeVCF {
   script: 
   """
   mkdir -p temp
-  bcftools concat -a ${ vcfFiles } -Oz -o temp-${ mergedVCF}.vcf.gz
+  bcftools concat --no-version -a ${ vcfFiles } -Oz -o temp-${ mergedVCF}.vcf.gz
   bcftools sort -T temp -Oz temp-${ mergedVCF}.vcf.gz -o ${ mergedVCF}.vcf.gz 
-  bcftools  index -t ${ mergedVCF}.vcf.gz
+  bcftools index -t ${ mergedVCF}.vcf.gz
   """
 }
diff --git a/nextflow/nf_modules/split_VCF.nf b/nextflow/nf_modules/split_VCF.nf
@@ -35,14 +35,14 @@ process splitVCF {
 
   script:
   """
-  bcftools view -r ${chr} ${vcf} -o ${prefix}.${chr}.vcf.gz -O z
+  bcftools view --no-version -r ${chr} ${vcf} -o ${prefix}.${chr}.vcf.gz -O z
   bcftools index -t ${prefix}.${chr}.vcf.gz
   
   if [[ ${bin_size} ]]; then 
     bcftools query -f'%CHROM\t%POS\n' ${prefix}.${chr}.vcf.gz | split -l ${bin_size}
     
     for file in x*; do 
-      bcftools view -T \${file} -Oz ${prefix}.${chr}.vcf.gz > ${prefix}.${chr}.\${file}.vcf.gz
+      bcftools view --no-version -T \${file} -Oz ${prefix}.${chr}.vcf.gz > ${prefix}.${chr}.\${file}.vcf.gz
       bcftools index -t ${prefix}.${chr}.\${file}.vcf.gz
     done