From ec9570521ba2edf40e1308c4ecbba606201ab56b Mon Sep 17 00:00:00 2001 From: chaopower Date: Mon, 15 Jan 2024 13:29:24 +0800 Subject: [PATCH] bug --- wdl/call_mutation.wdl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/wdl/call_mutation.wdl b/wdl/call_mutation.wdl index be8d16b..be3e023 100755 --- a/wdl/call_mutation.wdl +++ b/wdl/call_mutation.wdl @@ -308,12 +308,12 @@ task hotspot { -b $PUBLIC/hotspot/hotspot_delins.bed \ -o ${output_dir}/mutation/${name}.raw.hotspot.delins.vcf - vcf_operations.py ${output_dir}/mutation/${name}.raw.hotspot.vcf \ + vcf_operations.py ${raw_vcf} \ -b $PUBLIC/hotspot/hotspot_snpindel.bed \ -o ${output_dir}/mutation/${name}.raw.hotspot.snpindel.vcf \ -s - vcf_operations.py ${output_dir}/mutation/${name}.raw.hotspot.vcf \ + vcf_operations.py ${raw_vcf} \ -v $PUBLIC/hotspot/hotspot_snv.vcf \ -o ${output_dir}/mutation/${name}.raw.hotspot.snv.vcf @@ -455,7 +455,7 @@ task mutation_sum { fi { head -n 1 ${somatic_txt} ; tail -n +2 ${somatic_txt} ; tail -n +2 ${hotspot_txt} ;} |\ - { head -n 1 ; awk -F '\t' '{$1 = 1; OFS="\t" ; key=""; for (i=2; i<=NF-1; i++) { key = key $i "," } \ + { head -n 1 ; awk -F '\t' '{$1 = 1; OFS="\t" ; key=""; for (i=3; i<=7; i++) { key = key $i "," } \ if (key in data) { data[key] = data[key] ";" $NF; } \ else { data[key] = $0; }} END { for (i in data) { print data[i]; } }' ; } > \ ${output_dir}/mutation/${name}.snp_indel.somatic.hg19_multianno.filter.sum.txt