Fix species error variable

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)/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/url:=URI,length:=File_size,filename:=File_Name,md5:=MD5,Study_RID,Experiment_RID,Replicate_RID?limit=none"
         }
       }
     ]

workflow/rna-seq.nf

@@ -945,21 +945,21 @@ speciesError_fl.splitCsv(sep: ",", header: false).separate(
 )
 
 //  Replicate errors for multiple process inputs
-fastqCountError.into {
-  fastqCountError_checkMetadata
-  fastqCountError_uploadExecutionRun
-  fastqCountError_getRef
-  fastqCountError_alignData
-  fastqCountError_dedupData
-  fastqCountError_makeBigWig
-  fastqCountError_countData
-  fastqCountError_fastqc
-  fastqCountError_dataQC
-  fastqCountError_aggrQC
-  fastqCountError_uploadQC
-  fastqCountError_uploadProcessedFile
-  fastqCountError_uploadOutputBag
-  fastqCountError_failPreExecutionRun
+speciesError.into {
+  speciesError_checkMetadata
+  speciesError_uploadExecutionRun
+  speciesError_getRef
+  speciesError_alignData
+  speciesError_dedupData
+  speciesError_makeBigWig
+  speciesError_countData
+  speciesError_fastqc
+  speciesError_dataQC
+  speciesError_aggrQC
+  speciesError_uploadQC
+  speciesError_uploadProcessedFile
+  speciesError_uploadOutputBag
+  speciesError_failPreExecutionRun
 }
 
 /* 

workflow/scripts/bdbag_fetch.sh

@@ -10,5 +10,20 @@ then
     done
 elif [ "${3}" == "TEST" ]
 then
-    bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1} --debug
+    bdbag --materialize ${1} --debug
+    validateError=true
+    bdbag --validate full ${1} && validateError=false
+    if validateError
+    then
+        n=0
+        until [ "${n}" -ge "3" ]
+        do
+            bdbag --resolve-fetch missing --validate full ${1} --debug && validateError=false && break
+            n=$((n+1)) 
+            sleep 15
+        done
+    fi
+    if validateError
+    then
+        exit 1
 fi