diff --git a/runs/merged_isa_metadata/README.md b/runs/merged_isa_metadata/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..ceeaf9be121e5a15dc987ee4d719cfd156017279
--- /dev/null
+++ b/runs/merged_isa_metadata/README.md
@@ -0,0 +1,4 @@
+
+
+
+cwltool ../../workflows/merge_isa_metadata.cwl merge_isa_metadata.yml
\ No newline at end of file
diff --git a/workflows/merge_isa_metadata.yml b/runs/merged_isa_metadata/merge_isa_metadata.yml
similarity index 82%
rename from workflows/merge_isa_metadata.yml
rename to runs/merged_isa_metadata/merge_isa_metadata.yml
index 27806b37bcecb76072082d9b59c706795309468f..0a2a9fddd8162ca8ce0c904ed0f014892d5b9dc6 100644
--- a/workflows/merge_isa_metadata.yml
+++ b/runs/merged_isa_metadata/merge_isa_metadata.yml
@@ -1,7 +1,8 @@
 cores: 1
 r_script:
   class: File
-  path: ./merge_isa_metadata.R
+  path: ../../workflows/merge_isa_metadata.R
+# arc_root: ../
 arc_root: /Users/dominikbrilhaus/03_DataPLANT_gitlab/samplearc_rnaseq/
 in_isa_study: studies/TalinumFacultativeCAM/isa.study.xlsx:plant_growth
 in_isa_assay: assays/Talinum_RNASeq_minimal/isa.assay.xlsx:2EXT01_RNA:3ASY01_RNASeq
diff --git a/workflows/merge_isa_metadata.R b/workflows/merge_isa_metadata.R
index 4af0582c61dbd55afb9cd3f7eb014c0315157e96..c629683f77f98f73fd0ea8440cd7bdcddf8cfbe7 100644
--- a/workflows/merge_isa_metadata.R
+++ b/workflows/merge_isa_metadata.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env Rscript
 
 ################################################
-#### Test area
+#### Test area (Within R)
 ################################################
 
 # arc_root <- "~/03_DataPLANT_gitlab/samplearc_rnaseq/"
@@ -14,7 +14,6 @@
 ################################################
 
 library(openxlsx)
-# library(tidyverse)
 
 ################################################
 #### Read arguments from CLI
@@ -77,15 +76,15 @@ isa_merged <- isa_merged[, !apply(isa_merged, 2, function(x) {
 
 
 ################################################
-#### Write to file
+#### If it does not exist, create out dir
 ################################################
 
-## Create directory 
+
 dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
-# dir.create(out_folder, recursive = T, showWarnings = F)
 
-## Write 
-write.table(isa_merged, file = paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
 
+################################################
+#### Write table to file
+################################################
 
-# View(read.csv(paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t"))
+write.table(isa_merged, file = paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
\ No newline at end of file