From fb96fd356d7dba7b88b9eedc10fd4f3ede3a4f9d Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Tue, 2 Jan 2024 11:48:43 +0800
Subject: [PATCH] =?UTF-8?q?=E8=A1=80=E6=B6=B2qc?=
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---
 pipeline.wdl       |  3 +++
 wdl/alignment.wdl  |  2 ++
 wdl/statistics.wdl | 65 +++++++++++++++++++++++++++++++++++++++++-----
 3 files changed, 63 insertions(+), 7 deletions(-)

diff --git a/pipeline.wdl b/pipeline.wdl
index d9a4b81..09a6236 100644
--- a/pipeline.wdl
+++ b/pipeline.wdl
@@ -69,9 +69,12 @@ workflow pipeline {
         input:
             run=catecode['addAlignment'],
             tumor=tumor,
+            umi=umi,
             tumor_rmdup_bam=alignment.tumor_rmdup_bam,
+            tumor_sorted_bam=alignment.tumor_sorted_bam,
             normal=normal,
             normal_rmdup_bam=alignment.normal_rmdup_bam,
+            genecore_json=alignment.genecore_json,
             ref=ref,
             bed=bed,
             output_dir=workdir
diff --git a/wdl/alignment.wdl b/wdl/alignment.wdl
index f741df9..d53d89c 100755
--- a/wdl/alignment.wdl
+++ b/wdl/alignment.wdl
@@ -48,6 +48,7 @@ task markduplicates_genecore {
 
     output {
         String rmdup_bam = "${output_dir}/alignment/${name}.rmdup.bam"
+        String genecore_json = "${output_dir}/alignment/${name}_gencore.json"
     }
 }
 
@@ -202,5 +203,6 @@ workflow alignment {
         String normal_sorted_bam = "${output_dir}/alignment/${normal}.sorted.bam"
         String normal_rmdup_bam = "${output_dir}/alignment/${normal}.rmdup.bam"
         String normal_pileup = "${output_dir}/alignment/${normal}.pileup"
+        String genecore_json = "${output_dir}/alignment/${name}_gencore.json"
     }
 }
\ No newline at end of file
diff --git a/wdl/statistics.wdl b/wdl/statistics.wdl
index 09435a6..fa1c721 100755
--- a/wdl/statistics.wdl
+++ b/wdl/statistics.wdl
@@ -26,27 +26,78 @@ task run_statistics {
     }
 }
 
+task run_statistics_umi {
+    String name
+    String output_dir
+    String sortedBam
+    String rmdupBam
+    String genecore_json
+
+    String ref
+    String bed
+
+    command {
+
+        if [ ! -d ${output_dir}/qc/${name}_bamdst ];then
+        mkdir -p ${output_dir}/qc/${name}_bamdst
+        mkdir -p ${output_dir}/qc/${name}_sorted_bamdst
+        fi
+
+        samtools flagstat -@ 10 ${rmdupBam} >${output_dir}/qc/${name}.rmdup.flagstat
+        samtools stats --reference ${ref} -t ${bed} -@ 10 ${rmdupBam} > ${output_dir}/qc/${name}.rmdup.stat
+        bamdst -p ${bed} -o ${output_dir}/qc/${name}_bamdst ${rmdupBam}
+        bamdst -p ${bed} -o ${output_dir}/qc/${name}_sorted_bamdst ${sortedBam}
+
+        qc_stat_umi.py ${output_dir}/qc/${name}.json ${output_dir}/qc/${name}_bamdst/ ${output_dir}/qc/${name}_sorted_bamdst/ ${genecore_json} ${output_dir}/qc/${name}_qc.txt
+
+        #        InsertAndDepthStat.R \
+        #        ${output_dir}/qc/${name}_InsertAndDepthStat \
+        #        ${output_dir}/qc/${name}_bamdst/insertsize.plot \
+        #        ${output_dir}/qc/${name}_bamdst/depth_distribution.plot
+    }
+}
+
 workflow statistics {
     Boolean run=true
 
+    Boolean umi
+
     String tumor
     String tumor_rmdup_bam
+    String tumor_sorted_bam
 
     String? normal
     String? normal_rmdup_bam
 
+    String genecore_json
+
     String ref
     String bed
     String output_dir
 
     if (run) {
-        call run_statistics as runstatistics_tumor {
-            input:
-                name=tumor,
-                output_dir=output_dir,
-                rmdupBam=tumor_rmdup_bam,
-                ref=ref,
-                bed=bed
+        if (umi) {
+            call run_statistics_umi as runstatistics_umi_tumor {
+                input:
+                    name=tumor,
+                    output_dir=output_dir,
+                    rmdupBam=tumor_rmdup_bam,
+                    genecore_json=genecore_json,
+                    sortedBam=tumor_sorted_bam,
+                    ref=ref,
+                    bed=bed
+            }
+        }
+
+        if (!umi) {
+            call run_statistics as runstatistics_tumor {
+                input:
+                    name=tumor,
+                    output_dir=output_dir,
+                    rmdupBam=tumor_rmdup_bam,
+                    ref=ref,
+                    bed=bed
+            }
         }
 
         if (defined(normal)) {