Filter input bag export config to only get fastq's matching convention

CHANGELOG.md

@@ -8,6 +8,7 @@
 * Move fastqc process before trim to catch fastq errors (#107)
 * Only use fastq's that match *.R[1,2].fastq.gz naming convention (#107)
 * Add error output for no fastq's
+* Update input bag export config to only fetch fastq's that match *.R[1,2].fastq.gz naming convention
 
 *Known Bugs*
 * Override params (inputBag, fastq, species) aren't checked for integrity

workflow/conf/Replicate_For_Input_Bag.json

@@ -89,7 +89,7 @@
         "processor": "fetch",
         "processor_params": {
           "output_path": "assets/Study/{Study_RID}/Experiment/{Experiment_RID}/Replicate/{Replicate_RID}",
-          "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(RID)=(RNASeq:File:Replicate_RID)/File_Type=FastQ/url:=URI,length:=File_size,filename:=File_Name,md5:=MD5,Study_RID,Experiment_RID,Replicate_RID?limit=none"
+          "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(RID)=(RNASeq:File:Replicate_RID)/File_Type=FastQ/File_Name::ciregexp::%5B_.%5DR%5B12%5D%5C.fastq%5C.gz/url:=URI,length:=File_size,filename:=File_Name,md5:=MD5,Study_RID,Experiment_RID,Replicate_RID?limit=none"
         }
       }
     ]