From b68e85563723455ca78129b220ed833047503a09 Mon Sep 17 00:00:00 2001
From: mikaelamo <mikaelamoskov@hotmail.com>
Date: Fri, 4 Aug 2023 13:20:50 +0200
Subject: [PATCH] Removed forgotten file

---
 config/organise_runfolder.yml | 43 -----------------------------------
 1 file changed, 43 deletions(-)
 delete mode 100644 config/organise_runfolder.yml

diff --git a/config/organise_runfolder.yml b/config/organise_runfolder.yml
deleted file mode 100644
index bdadcfc..0000000
--- a/config/organise_runfolder.yml
+++ /dev/null
@@ -1,43 +0,0 @@
----
-#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
-