tmb 血液bug

codes/correct_umi_overlap_reads.py

@@ -74,8 +74,8 @@ def correct(chr, start, end, alt_base):
     for R in b:
         if len(list(dic[dic['read'] == R]['base'])) == 2:
             if list(dic[dic['read'] == R]['base'])[0] != list(dic[dic['read'] == R]['base'])[1]:
-                print(dic[dic['read'] == R]['base'])
-                print(dic[dic['read'] == R]['quality'])
+                # print(dic[dic['read'] == R]['base'])
+                # print(dic[dic['read'] == R]['quality'])
                 alt_reads.remove(R)
             else:
                 # if (list(dic[dic['read'] == R]['quality'])[0] >= 20 and list(dic[dic['read'] == R]['NM'])[0] < 4) or (

pipeline.wdl

@@ -105,7 +105,8 @@ workflow pipeline {
             output_dir=workdir,
             project=project,
             umi=umi,
-            file=call_mutation.somatic_anno_txt
+            file=call_mutation.somatic_anno_txt,
+            tumor_rmdup_bam=alignment.tumor_rmdup_bam
 
     }
 

wdl/tmb.wdl

@@ -26,6 +26,36 @@ task run_tmb {
     }
 }
 
+task run_tmb_umi {
+    String name
+    String file
+    String project
+    String sample_type
+    String output_dir
+    String tumor_rmdup_bam
+
+    command {
+        if [ ! -d ${output_dir}/tmb ];then
+        mkdir ${output_dir}/tmb
+        fi
+        filter_snpindel.pl \
+        ${file} \
+        ${output_dir}/tmb/${name}.tmb.pre.txt \
+        ${output_dir}/tmb/${name}.tmb.tag.txt \
+        ${project} \
+        ${sample_type} \
+        tmb
+
+        correct_umi_overlap_reads.py ${output_dir}/tmb/${name}.tmb.pre.txt ${tumor_rmdup_bam} ${output_dir}/tmb/${name}.tmb.txt
+
+
+    }
+
+    output {
+        String tmb_txt = "${output_dir}/tmb/${name}.tmb.txt"
+    }
+}
+
 workflow call_tmb {
 
     Boolean run=true
@@ -35,16 +65,31 @@ workflow call_tmb {
     String project
     String output_dir
     Boolean umi
+    String tumor_rmdup_bam
 
     if (run) {
-        call run_tmb {
+        if (umi) {
+            call run_tmb_umi {
             input:
                 name=name,
                 file=file,
                 project=project,
-                sample_type=if umi then 'c' else 't',
+                sample_type='c',
+                output_dir=output_dir,
+                tumor_rmdup_bam=tumor_rmdup_bam
+        }
+        }
+        if (!umi) {
+            call run_tmb {
+            input:
+                name=name,
+                file=file,
+                project=project,
+                sample_type='t',
                 output_dir=output_dir
         }
+        }
+
 
     }