From fd769afbc7bc324bd156da35d82f8e0dc89808a9 Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Mon, 8 Jan 2024 13:38:36 +0800
Subject: [PATCH] bug

---
 wdl/alignment.wdl     | 12 ++++++------
 wdl/call_mutation.wdl |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/wdl/alignment.wdl b/wdl/alignment.wdl
index aa99d0f..2947779 100755
--- a/wdl/alignment.wdl
+++ b/wdl/alignment.wdl
@@ -165,18 +165,18 @@ workflow alignment {
                     read1=normal_r1,
                     read2=normal_r2
             }
-            call markduplicates_picard as tumor_markduplicates_picard_control {
+            call markduplicates_picard as normal_markduplicates_picard_control {
                 input:
-                    name=tumor,
+                    name=normal,
                     ref=ref,
                     output_dir=output_dir,
                     sorted_bam=bwa_tumor_control.sorted_bam,
             }
 
             if (umi) {
-                call markduplicates_genecore as normal_markduplicates_genecore {
+                call markduplicates_genecore as tumor_markduplicates_genecore {
                     input:
-                        name=normal,
+                        name=tumor,
                         ref=ref,
                         output_dir=output_dir,
                         sorted_bam=bwa_normal_control.sorted_bam,
@@ -184,9 +184,9 @@ workflow alignment {
             }
 
             if (!umi) {
-                call markduplicates_picard as normal_markduplicates_picard {
+                call markduplicates_picard as tumor_markduplicates_picard {
                     input:
-                        name=normal,
+                        name=tumor,
                         ref=ref,
                         output_dir=output_dir,
                         sorted_bam=bwa_normal_control.sorted_bam,
diff --git a/wdl/call_mutation.wdl b/wdl/call_mutation.wdl
index e3bff3e..c5c65d2 100755
--- a/wdl/call_mutation.wdl
+++ b/wdl/call_mutation.wdl
@@ -267,7 +267,7 @@ task mutation_calling_tissue_control {
         vcf_add_tag_msi.pl ${output_dir}/mutation/${name}.raw.snp_indel.vcf ${output_dir}/mutation/${name}.raw.addtagmsi.snp_indel.vcf ${probe} t
 
         vcf_filter.py -i ${output_dir}/mutation/${name}.raw.addtagmsi.snp_indel.vcf \
-        -o ${output_dir}/mutation/${name}.snp_indel.somatic.vcf \AF[0] > 3*FORMAT/AF[1]
+        -o ${output_dir}/mutation/${name}.snp_indel.somatic.vcf
         -e 'INFO/STATUS="StrongSomatic" | ( INFO/STATUS="LikelySomatic" && FORMAT/AF[0] > 3*FORMAT/AF[1] )'
 
         vcf_filter.py -i ${output_dir}/mutation/${name}.raw.snp_indel.vcf \