Changed indentation in organise_runfolder.yml and moved the config to…

… new subdir config/organise_config/

config/organise_config/organise_runfolder.yml

@@ -0,0 +1,43 @@
+---
+#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/
+
+#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)/
+    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
+
+   #The MultiQC files
+   - source: <RUNFOLDER>/seqreports/project/*
+     destination: <ORGANISED>/(?P=projectid)/<RUNFOLDER_NAME>/
+     options:
+       required: True
+       symlink: True
+       regexp: (?P<projectid>[\w-]+)/(?P<RUNFOLDER_NAME>\w+)_(?P=projectid)_multiqc_report[\w.-]+
+
+
+
+#what we are lacking, and what might need to be created outside the config is:
+#1. checksums.md5
+#2. Encrypted samplesheet
+#As far as I know, these don't exist prior to organization.
+
+#  #hypothethical undetermined, needs an input of lane(s) connected to project
+#  #We will not include this at this point, as it requires additional input. Will maybe end up in its own config or something.
+#  - source: <RUNFOLDER>/Unaligned/Undetermined/Undetermined_S0_L<lanes>_R<read>_001.fastq.gz
+#    destination: <RUNFOLDER>/Unaligned/<PROJECT>/Undetermined/
+#    options:
+#      required: False
+#      symlink: True
+