there must be a better way for that arcRoot

runs/merged_isa_metadata/README.md

 
+# cwltool README
 
+## First cd into the (runs) folder, with the .yml file
 
-cwltool ../../workflows/merge_isa_metadata.cwl merge_isa_metadata.yml
\ No newline at end of file
+cd /Users/dominikbrilhaus/03_DataPLANT_gitlab/samplearc_rnaseq/runs/merged_isa_metadata
+
+## Let it flow
+
+```bash
+
+### store arc root (two levels up from here) as variable
+arc_root=$(echo ${PWD%/*/*})
+
+# arc_root=/Users/dominikbrilhaus/03_DataPLANT_gitlab/samplearc_rnaseq/
+
+### write a temporary yml
+cat merge_isa_metadata.yml > merge_isa_metadata_rooted.yml
+
+### add the arc root to that yml
+printf "\narc_root: $arc_root\n" >> merge_isa_metadata_rooted.yml
+
+### run with cwltool
+cwltool ../../workflows/merge_isa_metadata.cwl merge_isa_metadata_rooted.yml
+
+```

runs/merged_isa_metadata/merge_isa_metadata.yml

@@ -2,8 +2,6 @@ cores: 1
 r_script:
   class: File
   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
 out_folder: runs/merged_isa_metadata
\ No newline at end of file

runs/merged_isa_metadata/merge_isa_metadata_rooted.yml

+cores: 1
+r_script:
+  class: File
+  path: ../../workflows/merge_isa_metadata.R
+in_isa_study: studies/TalinumFacultativeCAM/isa.study.xlsx:plant_growth
+in_isa_assay: assays/Talinum_RNASeq_minimal/isa.assay.xlsx:2EXT01_RNA:3ASY01_RNASeq
+out_folder: runs/merged_isa_metadata
+arc_root: /Users/dominikbrilhaus/03_DataPLANT_gitlab/samplearc_rnaseq

workflows/merge_isa_metadata.R

@@ -26,8 +26,6 @@ in_isa_study <- args[2]
 in_isa_assay <- args[3]
 out_folder <- args[4]
 
-# setwd(arc_root)
-
 ################################################
 #### Read metadata from isa excel workbooks
 ################################################
@@ -36,12 +34,12 @@ isa_study <- unlist(strsplit(paste(arc_root, in_isa_study, sep = "/"), split = "
 isa_assay <- unlist(strsplit(paste(arc_root, in_isa_assay, sep = "/"), split = ":"))
 
 isa_sheets <- list()
-for(i in 2:length(isa_study))
+for (i in 2:length(isa_study))
 {
   isa_sheets[[length(isa_sheets) + 1]] <- readWorkbook(isa_study[1], isa_study[i], startRow = 1)
 }
 
-for(i in 2:length(isa_assay))
+for (i in 2:length(isa_assay))
 {
   isa_sheets[[length(isa_sheets) + 1]] <- readWorkbook(isa_assay[1], isa_assay[i], startRow = 1)
 }
@@ -52,20 +50,19 @@ for(i in 2:length(isa_assay))
 
 isa_merged <- isa_sheets[[1]]
 
-for(j in 2:length(isa_sheets))
+for (j in 2:length(isa_sheets))
 # for(j in 2)
 {
   isa_merged <- merge(isa_merged,
-                    isa_sheets[[j]],
-                    by.x = "Sample.Name",
-                    by.y = "Source.Name",
+    isa_sheets[[j]],
+    by.x = "Sample.Name",
+    by.y = "Source.Name",
   )
 
   # Rename duplicated Sample.Name column
 
   colnames(isa_merged)[which(colnames(isa_merged) == "Sample.Name")] <- paste("Sample.Name", j, sep = ".")
   colnames(isa_merged)[which(colnames(isa_merged) == "Sample.Name.y")] <- "Sample.Name"
-
 }
 
 
@@ -87,4 +84,4 @@ dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings =
 #### Write table to file
 ################################################
 
-write.table(isa_merged, file = paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
\ No newline at end of file
+write.table(isa_merged, file = paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")