indication

pipeline.wdl

@@ -191,7 +191,8 @@ workflow pipeline {
             name=tumor,
             normal=normal,
             output_dir=workdir,
-            cancer=cancer
+            cancer=cancer,
+            project=project
     }
 
     output {

script/indication.pl

@@ -2,8 +2,8 @@
 use strict;
 use warnings;
 
-my ($output_dir, $cancer_type) = @ARGV;
+die "useage:perl $0 output_dir cancer_type project" unless @ARGV == 3;
-die "useage:perl $0 output_dir cancer_type" unless @ARGV == 2;
+my ($output_dir, $cancer_type, $project) = @ARGV;
 
 my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
 
@@ -76,9 +76,38 @@ while (<THERAPY>) {
     }
 }
 
+my $muts_ref = info();
+
+my @muts = @$muts_ref;
+
 for my $gene (sort keys %therapy) {
+    # 是否检测
+    if (grep {$_ eq $gene} @muts) {
         print OUT "$gene\t", join("/", @{$therapy{$gene}}), "\t未检出变异\t", join("/", @{$cancer{$gene}}), "\n";
+    }
+
+}
+
+sub info {
+
+    open INFO, "$database_path/info.csv";
+    # 读取并解析表头
+    my $header = <INFO>;
+    chomp($header);
+    my @column_names = split(',', $header);
+    while (<INFO>) {
+        chomp;
+        my @line = split(/,/, $_);
+        # 将数据与表头对应
+        my %record;
+        @record{@column_names} = @line;
+        if ($record{'project'} eq $project) {
+            if ($record{'mutation'} ne "NA") {
+                @muts = split(/\//, $record{'mutation'});
+            }
+        }
+    }
+    return \@muts
 }
 
 
-

wdl/postprocess.wdl

@@ -10,12 +10,13 @@ task run_post {
     String? normal
     String output_dir
     String cancer
+    String project
     command <<<
 
         if [ ! -d ${output_dir}/report ];then
         mkdir ${output_dir}/report
         fi
-        indication.pl ${output_dir} ${cancer}
+        indication.pl ${output_dir} ${cancer} ${project}
         sample_post.py -s ${name} -o ${output_dir}
         postprocess.py -n ${name} -s ${normal} -c ${output_dir} -o ${output_dir}/report/${name}.merged_file.xlsx
     >>>
@@ -40,6 +41,7 @@ workflow call_postprocess {
     String? normal
     String output_dir
     String cancer
+    String project
 
     if (run) {
         call run_post {
@@ -54,7 +56,8 @@ workflow call_postprocess {
                 name=name,
                 normal=normal,
                 output_dir=output_dir,
-                cancer=cancer
+                cancer=cancer,
+                project=project
         }
     }