A running workflow with CWL!

Dockstore.json

@@ -1 +1,11 @@
-{}
+{
+"reads": [
+{
+"path":"/home/<your user name>/Seqware-BWA-Workflow/links/testData/sample_bam_sequence_synthetic_chr22_normal/9c414428-9446-11e3-86c1-ab5c73f0e08b/hg19.chr22.5x.normal.bam",
+"class":"File"
+}, 
+{"path":"/home/<your user name>/Seqware-BWA-Workflow/links/testData/sample_bam_sequence_synthetic_chr22_normal/4fb18a5a-9504-11e3-8d90-d1f1d69ccc24/hg19.chr22.5x.normal2.bam",
+"class":"File"
+}
+]
+}

scripts/run_seqware_workflow.pl

@@ -73,14 +73,10 @@
 # NOW FIND OUTPUT
 my $path = `ls -1t /datastore/ | grep 'oozie-' | head -1`;
 chomp $path;
-my $bam_path = "$path/data/merged_output.bam";
-my $bai_path = "$path/data/merged_output.bam.bai";
-my $ubam_path = "$path/data/merged_output.unmapped.bam";
-my $ubai_path = "$path/data/merged_output.unmapped.bam.bai";
 
 # MOVE THESE TO THE RIGHT PLACE
-system("mv $path/data/merged_output.bam* $cwd");
-system("mv $path/data/merged_output.unmapped.bam* $cwd");
+system("mv /datastore/$path/data/merged_output.bam* $cwd");
+system("mv /datastore/$path/data/merged_output.unmapped.bam* $cwd");
 
 # RETURN RESULT
 exit($error);