Update runfolder config

config/organise_config/organise_runfolder.yml

@@ -2,29 +2,30 @@
 #Input: runfolder_name
 
 #Currently named runfolderpath and runfolder to harmonize with rnaseq config by Monika, but for specific runfolder delivery, technically, these could be "merged" to one.
-runfolderpath: /proj/ngi2016001/incoming
-runfolder: <RUNFOLDERPATH>/<RUNFOLDER_NAME>
-organised: <RUNFOLDER>/Projects/
+variables:
+  runfolderpath: /proj/ngi2016001/incoming
+  runfolder: "{runfolderpath}/{runfolder_name}"
+  organised: "{runfolder}/Projects/"
 
 #current path is /proj/ngi2016001/incoming/<RUNFOLDER>/Projects/<PROJECT>/<RUNFOLDER>/
 #The following is based on that we are to keep the same directory structure as above.
 files_to_organize:
 
   #The fastq files
-  - source: <RUNFOLDER>/Unaligned/*  
-    destination: <ORGANISED>/(?P=projectid)/<RUNFOLDER_NAME>/Sample_(?P=samplename)/
+  - source: "{runfolder}/Unaligned/*"
+    destination: "{organised}/{projectid}/{runfolder_name}/Sample_{samplename}/"
     options:
       required: True
-      symlink: True
-      regexp: (?P<projectid>[\w-]+)/Sample_(?P<samplename>[\w-]+)/(?P=samplename)_S(?P<samplenumber>\d+)_L(?P<lanes>\d+)_R(?P<read>\d)_001.fastq.gz
+      link_type: softlink
+      regex: (?P<projectid>[\w-]+)/Sample_(?P<samplename>[\w-]+)/(?P=samplename)_S(?P<samplenumber>\d+)_L(?P<lanes>\d+)_R(?P<read>\d)_001.fastq.gz
 
    #The MultiQC files
-   - source: <RUNFOLDER>/seqreports/project/*
-     destination: <ORGANISED>/(?P=projectid)/<RUNFOLDER_NAME>/
+   - source: "{runfolder}/seqreports/project/*"
+     destination: "{organised}/{projectid}/<runfolder_name>/"
      options:
        required: True
-       symlink: True
-       regexp: (?P<projectid>[\w-]+)/(?P<RUNFOLDER_NAME>\w+)_(?P=projectid)_multiqc_report[\w.-]+
+       link_type: softlink
+       regexp: (?P<projectid>[\w-]+)/\w+_(?P=projectid)_multiqc_report[\w.-]+