use explicit list of pipeline dirs for inclusion

main.nf

@@ -90,29 +90,34 @@ Channel.fromPath("${samplesheetDir}/*", type: "dir", maxDepth: 1)
 }
 .set { samplesheet_ch }
 
-Channel.fromPath("${pipelinesDir}/*", type: "dir", maxDepth: 1)
+// Channel.fromPath("${pipelinesDir}/*", type: "dir", maxDepth: 1)
+Channel.from([
+    file("${pipelinesDir}/demux-nf"),
+    file("${pipelinesDir}/NGS580-nf"),
+    file("${pipelinesDir}/queue-stats"),
+    ])
 .map { dir ->
     def fullpath = new File("${dir}").getCanonicalPath()
     def basename = "${dir.baseName}"
     def type = "pipeline"
     return([ type, dir, basename, fullpath ])
 }
-.filter { items ->
-    def type = items[0]
-    def dir = items[1]
-    def basename = items[2]
-    def fullpath = items[3]
-
-    // do not run on these pipeline dirs
-    def names_to_ignore = [
-    "lyz-nf",
-    "NGS50-reporter",
-    "snsxt"
-    ]
-    def is_in_ignore_list = names_to_ignore.any { it.contains("${basename}") }
-    return(is_in_ignore_list)
-}
 .set { pipelines_dirs }
+// .filter { items ->
+//     def type = items[0]
+//     def dir = items[1]
+//     def basename = items[2]
+//     def fullpath = items[3]
+//
+//     // do not run on these pipeline dirs
+//     def names_to_ignore = [
+//     "lyz-nf",
+//     "NGS50-reporter",
+//     "snsxt"
+//     ]
+//     def is_in_ignore_list = names_to_ignore.any { it.contains("${basename}") }
+//     return(is_in_ignore_list)
+// }
 
 // ~~~~~ TASKS TO RUN ~~~~~ //
 // only create processes if not locked

nextflow.config

@@ -89,7 +89,7 @@ profiles {
          // try to prevent error: module: command not found by sourcing module config, and pausing to allow environment to finish populating
         process.beforeScript = ". /etc/profile.d/modules.sh; sleep 1; ${process.beforeScript}"
         // process.errorStrategy = "finish"
-        executor.queueSize = 4
+        executor.queueSize = 12
         params.syncServer = params.BigPurpleDataNode
     }
 }