Add missing file

modules/bids_patterns.nf

@@ -0,0 +1,40 @@
+def checkSesFolders() {
+    def Map entity = [:]
+    // Check if subject folders contain sessions ==================================
+    isSesFolder = true
+    // Emit false otherwise CHECKS ANAT FOLDER ONLY
+    Channel.fromPath( "$params.bids/sub*/ses*", type: 'dir', checkIfExists: true )
+            .ifEmpty { isSesFolder=false}
+
+    // Depending on whether the dataset uses session-level folders, 
+    // file-depths must be dynamically configured. 
+    // This is controlled by the ses_directory parameter.
+    // FitResultsSave_BIDS knows 
+    // how to deal with that based on SID passed by nextflow 
+    // when setenv('NEXTFLOW','1')
+
+    if (isSesFolder){
+        println "Session-level organization has been ENABLED."
+        entity.dirInputLevel = "**/**/"
+        entity.qmrlabSesFlag = "true"
+    }else{
+        println "Session-level organization has been DISABLED."
+        entity.dirInputLevel = "**/"
+        entity.qmrlabSesFlag = "false"
+    }
+
+    return entity
+}
+
+
+def getSubSesEntity(sid) {
+    def Map out = [:]
+    out.sub = ("${sid}" =~ /(sub[^_]+)/)[0][0]
+    if (isSesFolder){
+        out.ses = ("${sid}" =~ /(ses[^_]+)/)[0][0]
+        out.ses = out.ses + "/"
+    }else{
+        out.ses = ''
+    }
+    return out
+}