Mercurial > repos > estrain > srst2

changeset 3:8bf4865cc3e3 draft

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Uploaded
author estrain
date Sun, 19 May 2019 10:07:05 -0400
parents 6787d952242e
children 65cb7bb11e6b
files srst2v2.xml
diffstat 1 files changed, 31 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/srst2v2.xml	Sun May 19 07:36:55 2019 -0400
+++ b/srst2v2.xml	Sun May 19 10:07:05 2019 -0400
@@ -3,21 +3,44 @@
         <requirement type="package" version="0.2.0">srst2</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+
         #if $paired_conditional.sPaired == "paired"
-           ln -s $paired_conditional.fastq1 sample_1.fastq;
-           ln -s $paired_conditional.fastq2 sample_2.fastq;
+	  #if $paired_conditional.fastq1.is_of_type("fastq.gz")
+            zcat $paired_conditional.fastq1 > sample_1.fastq;
+            zcat $paired_conditional.fastq2 > sample_2.fastq;
+	  #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
+            zcat $paired_conditional.fastq1 > sample_1.fastq;
+            zcat $paired_conditional.fastq2 > sample_2.fastq;
+          #else
+            ln -s $paired_conditional.fastq1 sample_1.fastq;
+            ln -s $paired_conditional.fastq2 sample_2.fastq;
+          #end if
         #else if $paired_conditional.sPaired == "paired_coll" 
-           ln -s $paired_conditional.coll.forward sample_1.fastq;
-           ln -s $paired_conditional.coll.reverse sample_2.fastq;
+	  #if $paired_conditional.coll.forward.is_of_type("fastq.gz")
+            zcat $paired_conditional.coll.forward > sample_1.fastq;
+            zcat $paired_conditional.coll.reverse > sample_2.fastq;
+	  #else if $paired_conditional.coll.forward.is_of_type("fastqsanger.gz")
+            zcat $paired_conditional.coll.forward > sample_1.fastq;
+            zcat $paired_conditional.coll.reverse > sample_2.fastq;
+          #else 
+            ln -s $paired_conditional.coll.forward sample_1.fastq;
+            ln -s $paired_conditional.coll.reverse sample_2.fastq;
+          #end if
+        #else if $paired_conditional.sPaired == "single"
+	  #if $paired_conditional.fastq1.is_of_type("fastq.gz")
+            zcat $paired_conditional.fastq1 > sample_1.fastq;
+	  #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
+            zcat $paired_conditional.fastq1 > sample_1.fastq;
+          #else
+            ln -s $paired_conditional.fastq1 sample_1.fastq;
+          #end if
         #end if
 
         srst2
 
         #if $paired_conditional.sPaired == "single"
-            --input_se $paired_conditional.fastq1
-        #else if $paired_conditional.sPaired == "paired"
-            --input_pe sample_1.fastq sample_2.fastq
-        #else if $paired_conditional.sPaired == "paired_coll"
+            --input_se sample_1.fastq1
+        #else
             --input_pe sample_1.fastq sample_2.fastq
         #end if