execute from runs folder

runs/merged_isa_metadata/README.md

+
+
+
+cwltool ../../workflows/merge_isa_metadata.cwl merge_isa_metadata.yml
\ No newline at end of file

workflows/merge_isa_metadata.yml → runs/merged_isa_metadata/merge_isa_metadata.yml

 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

workflows/merge_isa_metadata.R

 #!/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