From 3006b700c4a3b0efe95902a8dbe24f804952d6d3 Mon Sep 17 00:00:00 2001
From: Jaeyoung Chun <jaeyoung.chun@gmail.com>
Date: Thu, 4 May 2017 15:38:30 -0400
Subject: [PATCH] Fix output collector

---
 mutect/outputs.yaml               | 6 +++---
 pindel/outputs.yaml               | 6 +++---
 somaticindeldetector/outputs.yaml | 8 ++++----
 vardict/outputs.yaml              | 6 +++---
 4 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/mutect/outputs.yaml b/mutect/outputs.yaml
index 25ca859..def08ec 100644
--- a/mutect/outputs.yaml
+++ b/mutect/outputs.yaml
@@ -4,8 +4,8 @@ outputs:
     outputBinding:
       glob: |
         ${
-          if (inputs.inputVcf )
-            return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.vcf';
+          if (inputs.inputVcf)
+            return inputs.inputVcf.basename.replace(".vcf","_STDfilter.vcf");
           return null;
         }
   txt:
@@ -14,6 +14,6 @@ outputs:
       glob: |
         ${
           if (inputs.inputTxt)
-            return inputs.inputTxt.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
+            return inputs.inputTxt.basename.replace(".txt","_STDfilter.txt");
           return null;
         }
diff --git a/pindel/outputs.yaml b/pindel/outputs.yaml
index 783b575..197f4ac 100644
--- a/pindel/outputs.yaml
+++ b/pindel/outputs.yaml
@@ -4,8 +4,8 @@ outputs:
     outputBinding:
       glob: |
         ${
-          if (inputs.inputVcf )
-            return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.vcf';
+          if (inputs.inputVcf)
+            return inputs.inputVcf.basename.replace(".vcf","_STDfilter.vcf");
           return null;
         }
   txt:
@@ -14,6 +14,6 @@ outputs:
       glob: |
         ${
           if (inputs.inputVcf)
-            return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
+            return inputs.inputVcf.basename.replace(".vcf","_STDfilter.txt");
           return null;
         }
diff --git a/somaticindeldetector/outputs.yaml b/somaticindeldetector/outputs.yaml
index 783b575..def08ec 100644
--- a/somaticindeldetector/outputs.yaml
+++ b/somaticindeldetector/outputs.yaml
@@ -4,8 +4,8 @@ outputs:
     outputBinding:
       glob: |
         ${
-          if (inputs.inputVcf )
-            return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.vcf';
+          if (inputs.inputVcf)
+            return inputs.inputVcf.basename.replace(".vcf","_STDfilter.vcf");
           return null;
         }
   txt:
@@ -13,7 +13,7 @@ outputs:
     outputBinding:
       glob: |
         ${
-          if (inputs.inputVcf)
-            return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
+          if (inputs.inputTxt)
+            return inputs.inputTxt.basename.replace(".txt","_STDfilter.txt");
           return null;
         }
diff --git a/vardict/outputs.yaml b/vardict/outputs.yaml
index 783b575..197f4ac 100644
--- a/vardict/outputs.yaml
+++ b/vardict/outputs.yaml
@@ -4,8 +4,8 @@ outputs:
     outputBinding:
       glob: |
         ${
-          if (inputs.inputVcf )
-            return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.vcf';
+          if (inputs.inputVcf)
+            return inputs.inputVcf.basename.replace(".vcf","_STDfilter.vcf");
           return null;
         }
   txt:
@@ -14,6 +14,6 @@ outputs:
       glob: |
         ${
           if (inputs.inputVcf)
-            return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
+            return inputs.inputVcf.basename.replace(".vcf","_STDfilter.txt");
           return null;
         }