diff --git a/.gitattributes b/.gitattributes
index 9992776affeb3d3878119e09bd8176a7fd14fcb0..7c3cf7781734b30a8e0cfccc6bdf9857f38f05a5 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -5,4 +5,4 @@
 /assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
 /assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
 /assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
-/runs/kallisto_index/kallisto_index filter=lfs diff=lfs merge=lfs -text
+/runs/kallisto_index/out/kallisto_index filter=lfs diff=lfs merge=lfs -text
diff --git a/runs/kallisto_collect/README.md b/runs/kallisto_collect/README.md
index 574080e009fc120d02514c5dfa15b6b6c602f00b..08cf2285fde86af02d22aee4681882eb2f1202e0 100644
--- a/runs/kallisto_collect/README.md
+++ b/runs/kallisto_collect/README.md
@@ -3,19 +3,11 @@
 
 ## First cd into the (runs) folder, with the .yml file
 
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_collect
+cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto_collect
 
 ## Let it flow
 
 ```bash
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux... 
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_collect.yml
-
 ### run with cwltool
-cwltool ../../workflows/kallisto_collect.cwl kallisto_collect.yml
-
+cwltool run.cwl kallisto_collect.yml
 ```
diff --git a/runs/kallisto_collect/kallisto_collect.yml b/runs/kallisto_collect/kallisto_collect.yml
index 1b300513c1481db8c9c0188d7dbd09f3acae4ad3..78c3462bef0722ff7793c0947165af574e0ccf4b 100644
--- a/runs/kallisto_collect/kallisto_collect.yml
+++ b/runs/kallisto_collect/kallisto_collect.yml
@@ -1,10 +1,10 @@
 cores: 1
-r_script:
+in_kallisto_results: 
+  class: Directory
+  path: ../kallisto_sleuth/out
+in_metadata_file: 
   class: File
-  path: ../../workflows/kallisto_collect.R
-in_kallisto_results: "runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results"
-in_metadata_file: "runs/merged_isa_metadata/merged_isa.tsv"
+  path: ../merged_isa_metadata/merged_isa.tsv
 in_metadata_sample: "Sample.Name.2"
 in_metadata_factor: "Factor..Photosynthesis.mode."
-out_folder: runs/kallisto_collect
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
\ No newline at end of file
+out_folder: out
diff --git a/runs/kallisto_collect/run.cwl b/runs/kallisto_collect/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..2736cc493acbad35870977c85eea6daec7a92edc
--- /dev/null
+++ b/runs/kallisto_collect/run.cwl
@@ -0,0 +1,30 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+inputs:
+  in_kallisto_results:
+    type: Directory
+  in_metadata_file:
+    type: File
+  in_metadata_sample:
+    type: string
+  in_metadata_factor:
+    type: string
+  out_folder:
+    type: string
+outputs:
+  out_dir:
+    type:
+      type: array
+      items: Directory
+    outputSource: kallisto_collect/outdir
+steps:
+  kallisto_collect:
+    run: ../../workflows/kallisto_collect/workflow.cwl
+    in:
+      in_kallisto_results: in_kallisto_results
+      in_metadata_file: in_metadata_file
+      in_metadata_sample: in_metadata_sample
+      in_metadata_factor: in_metadata_factor
+      out_folder: out_folder
+    out: [outdir]
diff --git a/runs/kallisto_index/README.md b/runs/kallisto_index/README.md
index 16475f8b77405c2dbb0e3b86c84bda9db3d4ccdd..ac67bff2d660c23469c2aa366693a9f42c3e7825 100644
--- a/runs/kallisto_index/README.md
+++ b/runs/kallisto_index/README.md
@@ -3,19 +3,11 @@
 
 ## First cd into the (runs) folder, with the .yml file
 
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index
+cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto_index
 
 ## Let it flow
 
 ```bash
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux... 
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_index.yml
-
 ### run with cwltool
-cwltool ../../workflows/kallisto_index.cwl kallisto_index.yml
-
+cwltool run.cwl kallisto_index.yml
 ```
diff --git a/runs/kallisto_index/kallisto_index.yml b/runs/kallisto_index/kallisto_index.yml
index 60f3a27f69a426983d158a83029b18693cf30c0c..37c668126ba083e52faee307fecd8ce59af2c0ba 100644
--- a/runs/kallisto_index/kallisto_index.yml
+++ b/runs/kallisto_index/kallisto_index.yml
@@ -1,7 +1,5 @@
 cores: 1
-sh_script:
+in_genome_ref:
   class: File
-  path: ../../workflows/kallisto_index.sh
-in_genome_ref: studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
-out_folder: runs/kallisto_index
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
+  path: ../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
+out_folder: ./out
diff --git a/runs/kallisto_index/kallisto_index b/runs/kallisto_index/out/kallisto_index
similarity index 100%
rename from runs/kallisto_index/kallisto_index
rename to runs/kallisto_index/out/kallisto_index
diff --git a/runs/kallisto_index/run.cwl b/runs/kallisto_index/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..a115ab7926f4c454ce8b95bc642571030b957066
--- /dev/null
+++ b/runs/kallisto_index/run.cwl
@@ -0,0 +1,21 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+inputs:
+  in_genome_ref:
+    type: File
+  out_folder:
+    type: string
+outputs:
+  out_dir:
+    type:
+      type: array
+      items: Directory
+    outputSource: kallisto_index/outdir
+steps:
+  kallisto_index:
+    run: ../../workflows/kallisto_index/workflow.cwl
+    in:
+      in_genome_ref: in_genome_ref
+      out_folder: out_folder
+    out: [outdir]
diff --git a/runs/kallisto_quant/README.md b/runs/kallisto_quant/README.md
index 7e0399169b09ac01f90709bcec1dd8d6e2e9694a..86c10cd181b91cefc59660d5f030a5a9db80cb98 100644
--- a/runs/kallisto_quant/README.md
+++ b/runs/kallisto_quant/README.md
@@ -3,19 +3,11 @@
 
 ## First cd into the (runs) folder, with the .yml file
 
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant
+cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto_quant
 
 ## Let it flow
 
 ```bash
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux... 
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_quant.yml
-
 ### run with cwltool
-cwltool ../../workflows/kallisto_quant.cwl kallisto_quant.yml
-
+cwltool run.cwl kallisto_quant.yml
 ```
diff --git a/runs/kallisto_quant/kallisto_quant.yml b/runs/kallisto_quant/kallisto_quant.yml
index 3a700dde637416106f587147d1a6104ecdd6326d..e5c7505ffe14ba3399cdc1d9f86db5e2ca50dd43 100644
--- a/runs/kallisto_quant/kallisto_quant.yml
+++ b/runs/kallisto_quant/kallisto_quant.yml
@@ -1,12 +1,12 @@
 cores: 4
-sh_script:
+out_folder: ./kallisto_results
+in_kallisto_index:
   class: File
-  path: ../../workflows/kallisto_quant.sh
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
-out_folder: runs/kallisto_quant/kallisto_results
-in_kallisto_index: runs/kallisto_index/kallisto_index
-in_fastq_folder: assays/Talinum_RNASeq_minimal/dataset
+  path: ../kallisto_index/out/kallisto_index
+in_fastq_dir: 
+  class: Directory
+  path: ../../assays/Talinum_RNASeq_minimal/dataset
 kallisto_bootstrap: 100
 kallisto_threads: 4
 kallisto_fragmentLength: 200
-kallisto_stdDev: 20
\ No newline at end of file
+kallisto_stdDev: 20
diff --git a/runs/kallisto_quant/run.cwl b/runs/kallisto_quant/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..af2bc99c83d6ae8a2c0db7775ce28f5cb009ecbd
--- /dev/null
+++ b/runs/kallisto_quant/run.cwl
@@ -0,0 +1,36 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+inputs:
+  out_folder:
+    type: string
+  in_kallisto_index:
+    type: File
+  in_fastq_dir:
+    type: Directory
+  kallisto_bootstrap:
+    type: int
+  kallisto_threads:
+    type: int
+  kallisto_fragmentLength:
+    type: int
+  kallisto_stdDev:
+    type: int
+outputs:
+  out_dir:
+    type:
+      type: array
+      items: Directory
+    outputSource: kallisto_quant/outdir
+steps:
+  kallisto_quant:
+    run: ../../workflows/kallisto_quant/workflow.cwl
+    in:
+      out_folder: out_folder
+      in_kallisto_index: in_kallisto_index
+      in_fastq_dir: in_fastq_dir
+      kallisto_bootstrap: kallisto_bootstrap
+      kallisto_threads: kallisto_threads
+      kallisto_fragmentLength: kallisto_fragmentLength
+      kallisto_stdDev: kallisto_stdDev
+    out: [outdir]
diff --git a/runs/kallisto_sleuth/README.md b/runs/kallisto_sleuth/README.md
index 05639e7e53b53e81a9f51f01627e43af130fec9c..8fc55827f0968cd26b3f30105bad7eeed2767ba2 100644
--- a/runs/kallisto_sleuth/README.md
+++ b/runs/kallisto_sleuth/README.md
@@ -3,19 +3,11 @@
 
 ## First cd into the (runs) folder, with the .yml file
 
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_sleuth
+cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto_sleuth
 
 ## Let it flow
 
 ```bash
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux... 
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_sleuth.yml
-
 ### run with cwltool
-cwltool ../../workflows/kallisto_sleuth.cwl kallisto_sleuth.yml
-
+cwltool run.cwl kallisto_sleuth.yml
 ```
diff --git a/runs/kallisto_sleuth/kallisto_sleuth.yml b/runs/kallisto_sleuth/kallisto_sleuth.yml
index 34364fd1b8f453cf2ec511b2549f890fd06442ba..49c11233026681aefe4d30351eaab03e21ba7477 100644
--- a/runs/kallisto_sleuth/kallisto_sleuth.yml
+++ b/runs/kallisto_sleuth/kallisto_sleuth.yml
@@ -1,7 +1,5 @@
 cores: 1
-r_script:
+in_sleuth:
   class: File
-  path: ../../workflows/kallisto_sleuth.R
-in_sleuth: runs/kallisto_collect/kallisto_sleuthObject.RData
-out_folder: runs/kallisto_sleuth
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
\ No newline at end of file
+  path: ../kallisto_collect/kallisto_sleuthObject.RData
+out_folder: out
diff --git a/runs/kallisto_sleuth/sleuth_dge.csv b/runs/kallisto_sleuth/out/sleuth_dge.csv
similarity index 100%
rename from runs/kallisto_sleuth/sleuth_dge.csv
rename to runs/kallisto_sleuth/out/sleuth_dge.csv
diff --git a/runs/kallisto_sleuth/run.cwl b/runs/kallisto_sleuth/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..dc8b77af8941b3988530ec0fa5c4ed74d52b0420
--- /dev/null
+++ b/runs/kallisto_sleuth/run.cwl
@@ -0,0 +1,21 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+inputs:
+  in_sleuth:
+    type: File
+  out_folder:
+    type: string
+outputs:
+  out_dir:
+    type:
+      type: array
+      items: Directory
+    outputSource: kallisto_sleuth/outdir
+steps:
+  kallisto_sleuth:
+    run: ../../workflows/kallisto_sleuth/workflow.cwl
+    in:
+      in_sleuth: in_sleuth
+      out_folder: out_folder
+    out: [outdir]
diff --git a/runs/merged_isa_metadata/README.md b/runs/merged_isa_metadata/README.md
index 59c24ded29d2efa45432c30c827d84606161102c..d15e984b6c20eae3bc7bdcf9257a861d9709e694 100644
--- a/runs/merged_isa_metadata/README.md
+++ b/runs/merged_isa_metadata/README.md
@@ -3,21 +3,12 @@
 
 ## First cd into the (runs) folder, with the .yml file
 
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/merged_isa_metadata
+cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/merged_isa_metadata
 
 
 ## Let it flow
 
 ```bash
-
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux... 
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" merge_isa_metadata.yml
-
 ### run with cwltool
-cwltool ../../workflows/merge_isa_metadata.cwl merge_isa_metadata.yml
-
+cwltool run.cwl merge_isa_metadata.yml
 ```
diff --git a/runs/merged_isa_metadata/merge_isa_metadata.yml b/runs/merged_isa_metadata/merge_isa_metadata.yml
index 0a52d038aaf9436fa63bd102e14eeb7066a4efb5..675e868f6bd804759cda137e747c21294817ab45 100644
--- a/runs/merged_isa_metadata/merge_isa_metadata.yml
+++ b/runs/merged_isa_metadata/merge_isa_metadata.yml
@@ -1,8 +1,8 @@
 cores: 1
-r_script:
+in_isa_study: 
   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/gitlab_dataplant/samplearc_rnaseq
\ No newline at end of file
+  path: ../../studies/TalinumFacultativeCAM/isa.study.xlsx
+in_isa_assay: 
+  class: File
+  path: ../../assays/Talinum_RNASeq_minimal/isa.assay.xlsx
+out_folder: out
diff --git a/runs/merged_isa_metadata/merged_isa.tsv b/runs/merged_isa_metadata/out/merged_isa.tsv
similarity index 62%
rename from runs/merged_isa_metadata/merged_isa.tsv
rename to runs/merged_isa_metadata/out/merged_isa.tsv
index 24bea101e89b855a18d5d294556d6d0f0ca4f170..166ac5e60bc061ce9934ac15313f44c8b4bca48e 100644
--- a/runs/merged_isa_metadata/merged_isa.tsv
+++ b/runs/merged_isa_metadata/out/merged_isa.tsv
@@ -1,7 +1,7 @@
 "Sample.Name.3"	"Sample.Name.2"	"Source.Name"	"Characteristics.[Organism]"	"Term.Source.REF.(NFDI4PSO:0000030)"	"Term.Accession.Number.(NFDI4PSO:0000030)"	"Characteristics.[Biological.replicate]"	"Term.Source.REF.(NFDI4PSO:0000042)"	"Term.Accession.Number.(NFDI4PSO:0000042)"	"Characteristics.[Organism.part]"	"Term.Source.REF.(NFDI4PSO:0000032)"	"Term.Accession.Number.(NFDI4PSO:0000032)"	"Characteristics.[age]"	"Term.Source.REF.(NFDI4PSO:0000033)"	"Term.Accession.Number.(NFDI4PSO:0000033)"	"Characteristics.[Developmental.Stage]"	"Term.Source.REF.(NFDI4PSO:0000070)"	"Term.Accession.Number.(NFDI4PSO:0000070)"	"Characteristics.[study.type]"	"Term.Source.REF.(PECO:0007231)"	"Term.Accession.Number.(PECO:0007231)"	"Parameter.[growth.chamber.company]"	"Term.Source.REF.().x"	"Term.Accession.Number.().x"	"Characteristics.[plant.growth.medium.exposure]"	"Term.Source.REF.(PECO:0007147)"	"Term.Accession.Number.(PECO:0007147)"	"Parameter.[Flower.pot]"	"Term.Source.REF.(#2).x"	"Term.Accession.Number.(#2).x"	"Characteristics.[Growth.day.length]"	"Term.Source.REF.(NFDI4PSO:0000041)"	"Term.Accession.Number.(NFDI4PSO:0000041)"	"Characteristics.[light.intensity.exposure]"	"Unit.x"	"Term.Source.REF.(PECO:0007224)"	"Term.Accession.Number.(PECO:0007224)"	"Characteristics.[Humidity.Day]"	"Unit.(#2).x"	"Term.Source.REF.(NFDI4PSO:0000005)"	"Term.Accession.Number.(NFDI4PSO:0000005)"	"Characteristics.[Humidity.Night]"	"Unit.(#3)"	"Term.Source.REF.(NFDI4PSO:0000006)"	"Term.Accession.Number.(NFDI4PSO:0000006)"	"Characteristics.[Temperature.Day]"	"Unit.(#4)"	"Term.Source.REF.(NFDI4PSO:0000007)"	"Term.Accession.Number.(NFDI4PSO:0000007)"	"Characteristics.[Temperature.Night]"	"Unit.(#5)"	"Term.Source.REF.(NFDI4PSO:0000008)"	"Term.Accession.Number.(NFDI4PSO:0000008)"	"Characteristics.[watering.exposure]"	"Term.Source.REF.(PECO:0007383)"	"Term.Accession.Number.(PECO:0007383)"	"Characteristics.[Sample.Collection.Date]"	"Term.Source.REF.(NFDI4PSO:0000075)"	"Term.Accession.Number.(NFDI4PSO:0000075)"	"Characteristics.[Sample.Collected.By]"	"Term.Source.REF.(NFDI4PSO:0000076)"	"Term.Accession.Number.(NFDI4PSO:0000076)"	"Characteristics.[Time.point]"	"Term.Source.REF.(NFDI4PSO:0000034)"	"Term.Accession.Number.(NFDI4PSO:0000034)"	"Parameter.[Sample.Collection.Method]"	"Term.Source.REF.(NFDI4PSO:0000009)"	"Term.Accession.Number.(NFDI4PSO:0000009)"	"Parameter.[Metabolism.quenching.method]"	"Term.Source.REF.(NFDI4PSO:0000010)"	"Term.Accession.Number.(NFDI4PSO:0000010)"	"Parameter.[Sample.storage]"	"Term.Source.REF.(NFDI4PSO:0000011)"	"Term.Accession.Number.(NFDI4PSO:0000011)"	"Factor.[Photosynthesis.mode]"	"Term.Source.REF.(#3)"	"Term.Accession.Number.(#3)"	"Parameter.[Bio.entity]"	"Term.Source.REF.(NFDI4PSO:0000012)"	"Term.Accession.Number.(NFDI4PSO:0000012)"	"Factor.[Biosource.amount]"	"Unit.y"	"Term.Source.REF.(NFDI4PSO:0000013)"	"Term.Accession.Number.(NFDI4PSO:0000013)"	"Parameter.[Extraction.method]"	"Term.Source.REF.(NFDI4PSO:0000054)"	"Term.Accession.Number.(NFDI4PSO:0000054)"	"Parameter.[Extraction.buffer]"	"Term.Source.REF.(NFDI4PSO:0000050)"	"Term.Accession.Number.(NFDI4PSO:0000050)"	"Parameter.[Extraction.buffer.volume]"	"Unit.(#2).y"	"Term.Source.REF.(NFDI4PSO:0000051)"	"Term.Accession.Number.(NFDI4PSO:0000051)"	"Factor.[RNA.quality.check]"	"Term.Source.REF.(NFDI4PSO:0000062)"	"Term.Accession.Number.(NFDI4PSO:0000062)"	"Parameter.[Library.strategy]"	"Term.Source.REF.(NFDI4PSO:0000035)"	"Term.Accession.Number.(NFDI4PSO:0000035)"	"Parameter.[Library.Selection]"	"Term.Source.REF.(NFDI4PSO:0000036)"	"Term.Accession.Number.(NFDI4PSO:0000036)"	"Parameter.[Library.layout]"	"Term.Source.REF.().y"	"Term.Accession.Number.().y"	"Parameter.[rRNA.Depletion]"	"Term.Source.REF.(#2).y"	"Term.Accession.Number.(#2).y"	"Parameter.[Library.preparation.kit]"	"Term.Source.REF.(NFDI4PSO:0000037)"	"Term.Accession.Number.(NFDI4PSO:0000037)"	"Parameter.[Library.preparation.kit.version]"	"Term.Source.REF.(NFDI4PSO:0000038)"	"Term.Accession.Number.(NFDI4PSO:0000038)"	"Factor.[Adapter.sequence]"	"Term.Source.REF.(NFDI4PSO:0000039)"	"Term.Accession.Number.(NFDI4PSO:0000039)"	"Unit"	"Term.Source.REF.(NFDI4PSO:0000016)"	"Term.Accession.Number.(NFDI4PSO:0000016)"	"Parameter.[Next.generation.sequencing.instrument.model]"	"Term.Source.REF.(NFDI4PSO:0000040)"	"Term.Accession.Number.(NFDI4PSO:0000040)"	"Parameter.[Base-calling.Software]"	"Term.Source.REF.(NFDI4PSO:0000017)"	"Term.Accession.Number.(NFDI4PSO:0000017)"	"Parameter.[Base-calling.Software.Version]"	"Term.Source.REF.(NFDI4PSO:0000018)"	"Term.Accession.Number.(NFDI4PSO:0000018)"	"Parameter.[Library.strand]"	"Term.Source.REF.(NFDI4PSO:0000020)"	"Term.Accession.Number.(NFDI4PSO:0000020)"	"Data.File.Name"	"Parameter.[Raw.data.file.format]"	"Term.Source.REF.(NFDI4PSO:0000021)"	"Term.Accession.Number.(NFDI4PSO:0000021)"
-"1"	"CAM_01_ext"	"CAM_01"	"DB_097"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep1"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"12 days drought"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"CAM"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	80	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"CAGATC"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
-"2"	"CAM_02_ext"	"CAM_02"	"DB_099"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep2"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"12 days drought"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"CAM"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	78	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.7 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"CTTGTA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
-"3"	"CAM_03_ext"	"CAM_03"	"DB_103"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep3"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"12 days drought"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"CAM"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	93	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 6.5 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"AGTCAA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
-"4"	"reC3_01_ext"	"reC3_01"	"DB_161"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep1"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"2 days rewatered"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"reC3"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	82	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.8 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"GTCCGC"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
-"5"	"reC3_02_ext"	"reC3_02"	"DB_163"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep2"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"2 days rewatered"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"reC3"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	96	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"GTGAAA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
-"6"	"reC3_03_ext"	"reC3_03"	"DB_165"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep3"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"2 days rewatered"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"reC3"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	78	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"GTGAAA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"1"	"CAM_01_ext"	"CAM_01"	"DB_097"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep1"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"12 days drought"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 °C"	"user-specific"	"user-specific"	"CAM"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	80	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"CAGATC"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"2"	"CAM_02_ext"	"CAM_02"	"DB_099"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep2"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"12 days drought"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 °C"	"user-specific"	"user-specific"	"CAM"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	78	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.7 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"CTTGTA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"3"	"CAM_03_ext"	"CAM_03"	"DB_103"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep3"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"12 days drought"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 °C"	"user-specific"	"user-specific"	"CAM"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	93	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 6.5 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"AGTCAA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"4"	"reC3_01_ext"	"reC3_01"	"DB_161"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep1"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"2 days rewatered"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 °C"	"user-specific"	"user-specific"	"reC3"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	82	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.8 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"GTCCGC"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"5"	"reC3_02_ext"	"reC3_02"	"DB_163"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep2"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"2 days rewatered"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 °C"	"user-specific"	"user-specific"	"reC3"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	96	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"GTGAAA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"6"	"reC3_03_ext"	"reC3_03"	"DB_165"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep3"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"2 days rewatered"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 °C"	"user-specific"	"user-specific"	"reC3"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	78	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"GTGAAA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
diff --git a/runs/merged_isa_metadata/run.cwl b/runs/merged_isa_metadata/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..9902aad273b2610e706c3f6dadcf7e8077ff7ff1
--- /dev/null
+++ b/runs/merged_isa_metadata/run.cwl
@@ -0,0 +1,24 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+inputs:
+  in_isa_study:
+    type: File
+  in_isa_assay:
+    type: File
+  out_folder:
+    type: string
+outputs:
+  out_dir:
+    type:
+      type: array
+      items: Directory
+    outputSource: merge_isa_metadata/outdir
+steps:
+  merge_isa_metadata:
+    run: ../../workflows/merge_isa_metadata/workflow.cwl
+    in:
+      in_isa_study: in_isa_study
+      in_isa_assay: in_isa_assay
+      out_folder: out_folder
+    out: [outdir]
diff --git a/runs/shiny_prep/README.md b/runs/shiny_prep/README.md
index 05639e7e53b53e81a9f51f01627e43af130fec9c..5891cd81ea7b5e0b50b6ed842f9fea9896405630 100644
--- a/runs/shiny_prep/README.md
+++ b/runs/shiny_prep/README.md
@@ -3,19 +3,11 @@
 
 ## First cd into the (runs) folder, with the .yml file
 
-cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_sleuth
+cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/shiny_prep
 
 ## Let it flow
 
 ```bash
-### store arc root (two levels up from here) as variable
-arc_root=$(echo ${PWD%/*/*})
-
-### replace arc root line in yml (specific to the machine from where this is run)
-### not sure, if this works on linux... 
-sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_sleuth.yml
-
 ### run with cwltool
-cwltool ../../workflows/kallisto_sleuth.cwl kallisto_sleuth.yml
-
+cwltool run.cwl shiny_prep.yml
 ```
diff --git a/runs/shiny_prep/out/shiny_prep.RData b/runs/shiny_prep/out/shiny_prep.RData
new file mode 100644
index 0000000000000000000000000000000000000000..05ad3fdef0add3ebd7bb6a027e4f7b575e33bb22
Binary files /dev/null and b/runs/shiny_prep/out/shiny_prep.RData differ
diff --git a/runs/shiny_prep/run.cwl b/runs/shiny_prep/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..4f5b2adc81b5e022925d3e753a1531d528e867a1
--- /dev/null
+++ b/runs/shiny_prep/run.cwl
@@ -0,0 +1,21 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+inputs:
+  out_folder:
+    type: string
+  in_kallisto_df:
+    type: File
+outputs:
+  out_dir:
+    type:
+      type: array
+      items: Directory
+    outputSource: shiny_prep/outdir
+steps:
+  shiny_prep:
+    run: ../../workflows/shiny_prep/workflow.cwl
+    in:
+      in_kallisto_df: in_kallisto_df
+      out_folder: out_folder
+    out: [outdir]
diff --git a/runs/shiny_prep/shiny_prep.RData b/runs/shiny_prep/shiny_prep.RData
deleted file mode 100644
index 258a091981fee5ee5389d9e76ca25e2a237768b8..0000000000000000000000000000000000000000
Binary files a/runs/shiny_prep/shiny_prep.RData and /dev/null differ
diff --git a/runs/shiny_prep/shiny_prep.yml b/runs/shiny_prep/shiny_prep.yml
index a8fec1d28132c8b86ab7e4264eae03acf7d79e2d..60c9636bed76b7f71ec8609c0c6c05cd0ed41085 100644
--- a/runs/shiny_prep/shiny_prep.yml
+++ b/runs/shiny_prep/shiny_prep.yml
@@ -1,7 +1,5 @@
 cores: 1
-r_script:
+in_kallisto_df:
   class: File
-  path: ../../workflows/shiny_prep.R
-in_kallisto_df: runs/kallisto_collect/kallisto_df.csv
-out_folder: runs/shiny_prep
-arc_root: /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq
+  path: ../kallisto_collect/kallisto_df.csv
+out_folder: out
diff --git a/workflows/install_dependencies/install_cwl.md b/workflows/install_dependencies/install_cwl.md
deleted file mode 100644
index d812962a3932a710221301d08205e47345bc95a2..0000000000000000000000000000000000000000
--- a/workflows/install_dependencies/install_cwl.md
+++ /dev/null
@@ -1,13 +0,0 @@
-
-# CWL Installation (MacOS)
-
-Docs: https://www.commonwl.org/
-GitHub: https://github.com/common-workflow-language/cwltool
-
-## Install CWL via conda
-
-> requires conda installation, which is a whole different story. Good luck.
-
-```bash
-conda install -c conda-forge cwltool
-```
diff --git a/workflows/install_dependencies/install_kallisto.md b/workflows/install_dependencies/install_kallisto.md
deleted file mode 100644
index 121b9f229d207352c3529e572286b3bd34b3f2f9..0000000000000000000000000000000000000000
--- a/workflows/install_dependencies/install_kallisto.md
+++ /dev/null
@@ -1,13 +0,0 @@
-
-# Kallisto Installation
-
-- Docs: http://pachterlab.github.io/kallisto/manual.html
-- GitHub: https://github.com/pachterlab/kallisto
-
-## MacOS Installation via conda
-
-see: https://anaconda.org/bioconda/kallisto
-
-```bash
-conda install -c bioconda kallisto
-```
diff --git a/workflows/install_dependencies/install_r_packages.R b/workflows/install_dependencies/install_r_packages.R
deleted file mode 100644
index fdb1eb1afb2ded3fb31d9f59a4487ce6a028163b..0000000000000000000000000000000000000000
--- a/workflows/install_dependencies/install_r_packages.R
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env Rscript
-
-################################################
-### Installation of R dependencies #############
-################################################
-
-### Default (CRAN)
-
-if(!"tidyverse" %in% row.names(installed.packages())){install.packages("tidyverse")}
-if(!"jsonlite" %in% row.names(installed.packages())){install.packages("jsonlite")}
-if(!"openxlsx" %in% row.names(installed.packages())){install.packages("openxlsx")}
-if(!"kableExtra" %in% row.names(installed.packages())){install.packages("kableExtra")}
-if(!"shiny" %in% row.names(installed.packages())){install.packages("shiny")}
-if(!"RColorBrewer" %in% row.names(installed.packages())){install.packages("RColorBrewer")}
-
-### From BiocManager
-
-if (!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}
-if(!"BiocManager" %in% row.names(installed.packages())){BiocManager::install()}
-if(!"devtools" %in% row.names(installed.packages())){BiocManager::install("devtools")}
-if(!"sleuth" %in% row.names(installed.packages())){BiocManager::install("pachterlab/sleuth")}
-
-### Test load packages
-
-library(tidyverse)
-library(jsonlite)
-library(openxlsx)
-library(sleuth)
-library(kableExtra)
-library(shiny)
-library(RColorBrewer)
diff --git a/workflows/kallisto_collect.R b/workflows/kallisto_collect/kallisto_collect.R
similarity index 75%
rename from workflows/kallisto_collect.R
rename to workflows/kallisto_collect/kallisto_collect.R
index b52176342b317b3c38a0f1359c2d7ad171cd9fe1..6c221c29fee6b3df1392bb2878cba7e647e304cf 100644
--- a/workflows/kallisto_collect.R
+++ b/workflows/kallisto_collect/kallisto_collect.R
@@ -4,7 +4,7 @@
 #### CWL-independent tests
 ################################################
 
-# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq/"
+# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq_adrian/"
 # in_kallisto_results <- "runs/kallisto_quant/kallisto_results"
 # in_metadata_file <- "runs/merged_isa_metadata/merged_isa.tsv"
 # in_metadata_sample <- "Sample.Name.2"
@@ -25,31 +25,30 @@ library(jsonlite)
 
 args <- commandArgs(trailingOnly = T)
 
-arc_root <- args[1]
-in_kallisto_results <- args[2]
-in_metadata_file <- args[3]
-in_metadata_sample <- args[4]
-in_metadata_factor <- args[5]
-out_folder <- args[6]
+in_kallisto_results <- args[1]
+in_metadata_file <- args[2]
+in_metadata_sample <- args[3]
+in_metadata_factor <- args[4]
+out_folder <- args[5]
 
 
 ################################################
 #### If it does not exist, create out dir
 ################################################
 
-dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
+dir.create(out_folder, recursive = T, showWarnings = F)
 
 ################################################
 #### Read ISA sample metadata
 ################################################
 
-samples <- read.table(file = paste(arc_root, in_metadata_file, sep = "/"), sep = "\t")
+samples <- read.table(file = in_metadata_file, sep = "\t")
 
 ################################################
 #### Read Kallisto results
 ################################################
 
-base_dir <- paste(arc_root, in_kallisto_results, sep = "/")
+base_dir <- in_kallisto_results
 
 # A list of paths to the kallisto results indexed by the sample IDs is collated with
 kal_dirs <- dir(base_dir, full.names = T) ## Sleuth requires full paths
@@ -67,7 +66,7 @@ s2c <- merge(s2c, path_df, by = "out_name")
 
 so <- sleuth_prep(s2c, full_model = ~condition, num_cores = 1)
 
-save(so, file = paste(arc_root, out_folder, "kallisto_sleuthObject.RData", sep = "/"))
+save(so, file = paste(out_folder, "kallisto_sleuthObject.RData", sep = "/"))
 
 
 ################################################
@@ -78,13 +77,13 @@ save(so, file = paste(arc_root, out_folder, "kallisto_sleuthObject.RData", sep =
 expression_data <- kallisto_table(so)
 
 ## write to file
-write.csv(expression_data, paste(arc_root, out_folder, "/kallisto_df.csv", sep = "/"), row.names = F)
+write.csv(expression_data, paste(out_folder, "/kallisto_df.csv", sep = "/"), row.names = F)
 
 ## as tpm matrix (gene x sample)
 tpm_table <- pivot_wider(expression_data, id_cols = target_id, names_from = sample, values_from = tpm)
 
 ## write to file
-write.csv(tpm_table, paste(arc_root, out_folder, "/kallisto_tpmMatrix.csv", sep = "/"), row.names = F)
+write.csv(tpm_table, paste(out_folder, "/kallisto_tpmMatrix.csv", sep = "/"), row.names = F)
 
 ################################################
 #### Summarize mapping stats
@@ -99,4 +98,4 @@ for (i in dir(kal_dirs, pattern = ".json", full.names = T))
   mapping_stats <- rbind(mapping_stats, z)
 }
 
-write.csv(mapping_stats, paste(arc_root, out_folder, "/kallisto_mappingStats.csv", sep = "/"), row.names = F)
+write.csv(mapping_stats, paste(out_folder, "/kallisto_mappingStats.csv", sep = "/"), row.names = F)
diff --git a/workflows/kallisto_collect.cwl b/workflows/kallisto_collect/workflow.cwl
similarity index 66%
rename from workflows/kallisto_collect.cwl
rename to workflows/kallisto_collect/workflow.cwl
index 8e3064c8dae6adb671d4daa9bded1894915f32e4..b5ed0f7fe34a6a740b6986efc079473186ad0c11 100644
--- a/workflows/kallisto_collect.cwl
+++ b/workflows/kallisto_collect/workflow.cwl
@@ -1,38 +1,40 @@
 #!/usr/bin/env cwl-runner
-
 cwlVersion: v1.2
 class: CommandLineTool
-
+hints:
+  DockerRequirement:
+    dockerPull: zimmera95/rnaseq:latest
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - class: File
+        location: kallisto_collect.R
+baseCommand:
+- Rscript
+arguments:
+  - position: 0
+    valueFrom: kallisto_collect.R
 inputs:
-- id: r_script
-  type: File
-  inputBinding:
-    position: 0
-- id: arc_root
-  type: string
-  inputBinding:
-    position: 1
 - id: in_kallisto_results
-  type: string
+  type: Directory
   inputBinding:
-    position: 2
+    position: 1
 - id: in_metadata_file
-  type: string
+  type: File
   inputBinding:
-    position: 3
+    position: 2
 - id: in_metadata_sample
   type: string
   inputBinding:
-    position: 4
+    position: 3
 - id: in_metadata_factor
   type: string
   inputBinding:
-    position: 5
+    position: 4
 - id: out_folder
   type: string
   inputBinding:
-    position: 6
-
+    position: 5
 outputs:
 - id: outdir
   type:
@@ -40,6 +42,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
\ No newline at end of file
diff --git a/workflows/kallisto_index.sh b/workflows/kallisto_index/kallisto_index.sh
old mode 100755
new mode 100644
similarity index 85%
rename from workflows/kallisto_index.sh
rename to workflows/kallisto_index/kallisto_index.sh
index 6cd3e178fa47e59af1e430a16e3def895dcefb37..c7cb12d292e64b8334a4cb1a80a833023c226dc6
--- a/workflows/kallisto_index.sh
+++ b/workflows/kallisto_index/kallisto_index.sh
@@ -16,9 +16,8 @@
 #### Read arguments from CLI
 ################################################
 
-arc_root=$1
-in_genome_ref=$2
-out_folder=$3
+in_genome_ref=$1
+out_folder=$2
 
 ################################################
 #### Print version and citation to test kallisto 
@@ -31,11 +30,10 @@ kallisto cite
 #### If it does not exist, create out dir
 ################################################
 
-mkdir -p "$arc_root/$out_folder/"
-
+mkdir -p $out_folder
 
 ################################################
 #### Build kallisto index
 ################################################
 
-kallisto index -i "$arc_root/$out_folder/kallisto_index" "$arc_root/$in_genome_ref"
+kallisto index -i $out_folder/kallisto_index $in_genome_ref
diff --git a/workflows/kallisto_index.cwl b/workflows/kallisto_index/workflow.cwl
similarity index 57%
rename from workflows/kallisto_index.cwl
rename to workflows/kallisto_index/workflow.cwl
index a6389de36bedc4d46d297b71c7dabd50ed07e200..32635f746d02b1061a0fe8d020045d2afe93b399 100644
--- a/workflows/kallisto_index.cwl
+++ b/workflows/kallisto_index/workflow.cwl
@@ -1,26 +1,28 @@
 #!/usr/bin/env cwl-runner
-
 cwlVersion: v1.2
 class: CommandLineTool
-
+hints:
+  DockerRequirement:
+    dockerPull: zlskidmore/kallisto:0.48.0
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - class: File
+        location: kallisto_index.sh
+baseCommand:
+- bash
+arguments:
+  - position: 0
+    valueFrom: ./kallisto_index.sh
 inputs:
-- id: sh_script
+- id: in_genome_ref
   type: File
-  inputBinding:
-    position: 0
-- id: arc_root
-  type: string
   inputBinding:
     position: 1
-- id: in_genome_ref
-  type: string
-  inputBinding:
-    position: 2
 - id: out_folder
   type: string
   inputBinding:
-    position: 3
-
+    position: 2
 outputs:
 - id: outdir
   type:
@@ -28,6 +30,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- bash
\ No newline at end of file
diff --git a/workflows/kallisto_quant.sh b/workflows/kallisto_quant/kallisto_quant.sh
old mode 100755
new mode 100644
similarity index 78%
rename from workflows/kallisto_quant.sh
rename to workflows/kallisto_quant/kallisto_quant.sh
index c1217416f77460b75944ccf50bb7cf9632a93ba8..124698c9db7ad01a8e73bc3a371ac69221e576d7
--- a/workflows/kallisto_quant.sh
+++ b/workflows/kallisto_quant/kallisto_quant.sh
@@ -20,26 +20,25 @@
 #### Read arguments from CLI
 ################################################
 
-arc_root=$1
-out_folder=$2
-in_kallisto_index=$3
-in_fastq_folder=$4
-kallisto_bootstrap=$5
-kallisto_threads=$6
-kallisto_fragmentLength=$7
-kallisto_stdDev=$8
+out_folder=$1
+in_kallisto_index=$2
+in_fastq_folder=$3
+kallisto_bootstrap=$4
+kallisto_threads=$5
+kallisto_fragmentLength=$6
+kallisto_stdDev=$7
 
 ################################################
 #### If it does not exist, create out dir
 ################################################
 
-mkdir -p "$arc_root/$out_folder/"
+mkdir -p "$out_folder"
 
 ################################################
 #### Store fastq files in variable
 ################################################
 
-fastq_files=$(ls "${arc_root}"/"${in_fastq_folder}"/*fastq*)
+fastq_files=$(ls "${in_fastq_folder}"/*fastq*)
 
 ################################################
 #### Loop over fastq files and quantify reads
@@ -52,7 +51,7 @@ for j in $fastq_files; do
 	
 	echo $sampleName
 	
-	kallisto quant --single -b $kallisto_bootstrap -t $kallisto_threads -l $kallisto_fragmentLength -s $kallisto_stdDev -i "$arc_root/$in_kallisto_index" -o "$arc_root/$out_folder/$sampleName" $j
+	kallisto quant --single -b $kallisto_bootstrap -t $kallisto_threads -l $kallisto_fragmentLength -s $kallisto_stdDev -i "$in_kallisto_index" -o "$out_folder/$sampleName" $j
 
 	echo 'Kallisto done'
 
diff --git a/workflows/kallisto_quant.cwl b/workflows/kallisto_quant/workflow.cwl
similarity index 70%
rename from workflows/kallisto_quant.cwl
rename to workflows/kallisto_quant/workflow.cwl
index 9259357a2df7043a94a49eba13d0d1b1f534db28..1041d7325d1c14ee4b634da642844da1a34f1ea8 100644
--- a/workflows/kallisto_quant.cwl
+++ b/workflows/kallisto_quant/workflow.cwl
@@ -1,45 +1,48 @@
 #!/usr/bin/env cwl-runner
-
 cwlVersion: v1.2
 class: CommandLineTool
-
+hints:
+  DockerRequirement:
+    dockerPull: zlskidmore/kallisto:0.48.0
+requirements:
+- class: InitialWorkDirRequirement
+  listing:
+  - class: File
+    location: kallisto_quant.sh
+baseCommand:
+- bash
+arguments:
+- position: 0
+  valueFrom: ./kallisto_quant.sh
 inputs:
-- id: sh_script
-  type: File
-  inputBinding:
-    position: 0
-- id: arc_root
+- id: out_folder
   type: string
   inputBinding:
     position: 1
-- id: out_folder
-  type: string
+- id: in_kallisto_index
+  type: File
   inputBinding:
     position: 2
-- id: in_kallisto_index
-  type: string
+- id: in_fastq_dir
+  type: Directory
   inputBinding:
     position: 3
-- id: in_fastq_folder
-  type: string
-  inputBinding:
-    position: 4
 - id: kallisto_bootstrap
   type: int
   inputBinding:
-    position: 5
+    position: 4
 - id: kallisto_threads
   type: int
   inputBinding:
-    position: 6
+    position: 5
 - id: kallisto_fragmentLength
   type: int
   inputBinding:
-    position: 7
+    position: 6
 - id: kallisto_stdDev
   type: int
   inputBinding:
-    position: 8
+    position: 7
 
 outputs:
 - id: outdir
@@ -48,6 +51,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- bash
diff --git a/workflows/kallisto_sleuth.cwl b/workflows/kallisto_sleuth.cwl
deleted file mode 100644
index 6f427261e5ec6da3dce2b916d2fcfc25659eff7a..0000000000000000000000000000000000000000
--- a/workflows/kallisto_sleuth.cwl
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.2
-class: CommandLineTool
-
-inputs:
-- id: r_script
-  type: File
-  inputBinding:
-    position: 0
-- id: arc_root
-  type: string
-  inputBinding:
-    position: 1
-- id: in_sleuth
-  type: string
-  inputBinding:
-    position: 2
-- id: out_folder
-  type: string
-  inputBinding:
-    position: 3
-
-outputs:
-- id: outdir
-  type:
-    type: array
-    items: Directory
-  outputBinding:
-    glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
\ No newline at end of file
diff --git a/workflows/kallisto_sleuth.R b/workflows/kallisto_sleuth/kallisto_sleuth.R
similarity index 80%
rename from workflows/kallisto_sleuth.R
rename to workflows/kallisto_sleuth/kallisto_sleuth.R
index ec3a84afe7aec0e9bab0b621c113e23e177a83bd..688904d0b3d69b94b474587583d8030122c218f6 100644
--- a/workflows/kallisto_sleuth.R
+++ b/workflows/kallisto_sleuth/kallisto_sleuth.R
@@ -1,5 +1,4 @@
 #!/usr/bin/env Rscript
-
 ################################################
 ### Diff. gene expression with sleuth ##########
 ################################################
@@ -8,37 +7,34 @@
 #### CWL-independent tests
 ################################################
 
-# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq/"
+# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq_adrian/"
 # in_sleuth <- "runs/kallisto_collect/kallisto_sleuthObject.RData"
 # out_folder <- "runs/kallisto_sleuth"
 
 ################################################
 #### Load required library
 ################################################
-
 library(sleuth)
-
 ################################################
 #### Read arguments from CLI
 ################################################
 
 args <- commandArgs(trailingOnly = T)
 
-arc_root <- args[1]
-in_sleuth <- args[2]
-out_folder <- args[3]
+in_sleuth <- args[1]
+out_folder <- args[2]
 
 ################################################
 #### If it does not exist, create out dir
 ################################################
 
-dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
+dir.create(out_folder, recursive = T, showWarnings = F)
 
 ################################################
 #### Load sleuth object
 ################################################
 
-load(file = paste(arc_root, in_sleuth, sep = "/"))
+load(file = in_sleuth)
 
 ################################################
 #### Run sleuth fit
@@ -55,4 +51,4 @@ sleuth_table <- sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
 #### write to file
 ################################################
 
-write.csv(sleuth_table, paste(arc_root, out_folder, "sleuth_dge.csv", sep = "/"), row.names = F)
+write.csv(sleuth_table, paste(out_folder, "sleuth_dge.csv", sep = "/"), row.names = F)
diff --git a/workflows/kallisto_sleuth/workflow.cwl b/workflows/kallisto_sleuth/workflow.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..48ac0b12fa9b8a22f117d806bc0dd196a3319d35
--- /dev/null
+++ b/workflows/kallisto_sleuth/workflow.cwl
@@ -0,0 +1,33 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+  DockerRequirement:
+    dockerPull: zimmera95/rnaseq:latest
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - class: File
+        location: kallisto_sleuth.R
+baseCommand:
+- Rscript
+arguments:
+  - position: 0
+    valueFrom: kallisto_sleuth.R
+inputs:
+  - id: in_sleuth
+    type: File
+    inputBinding:
+      position: 1
+  - id: out_folder
+    type: string
+    inputBinding:
+      position: 2
+outputs:
+- id: outdir
+  type:
+    type: array
+    items: Directory
+  outputBinding:
+    glob: $(runtime.outdir)/$(inputs.out_folder)
diff --git a/workflows/merge_isa_metadata.R b/workflows/merge_isa_metadata/merge_isa_metadata.R
similarity index 80%
rename from workflows/merge_isa_metadata.R
rename to workflows/merge_isa_metadata/merge_isa_metadata.R
index 5af105c569fe6b23a20b25e53e82ef80eb76b787..a4784c84bc663056058b76b127233fa5cfe531e8 100644
--- a/workflows/merge_isa_metadata.R
+++ b/workflows/merge_isa_metadata/merge_isa_metadata.R
@@ -4,7 +4,7 @@
 #### CWL-independent tests
 ################################################
 
-# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq/"
+# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq_adrian/"
 # 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"
@@ -21,17 +21,18 @@ library(openxlsx)
 
 args <- commandArgs(trailingOnly = T)
 
-arc_root <- args[1]
-in_isa_study <- args[2]
-in_isa_assay <- args[3]
-out_folder <- args[4]
+in_isa_study <- paste(args[1], ":plant_growth", sep="")
+print(in_isa_study)
+in_isa_assay <- paste(args[2], ":2EXT01_RNA:3ASY01_RNASeq", sep="")
+print(in_isa_assay)
+out_folder <- args[3]
 
 ################################################
 #### Read metadata from isa excel workbooks
 ################################################
 
-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_study <- unlist(strsplit(in_isa_study, split = ":"))
+isa_assay <- unlist(strsplit(in_isa_assay, split = ":"))
 
 isa_sheets <- list()
 for (i in 2:length(isa_study))
@@ -76,12 +77,10 @@ isa_merged <- isa_merged[, !apply(isa_merged, 2, function(x) {
 #### If it does not exist, create out dir
 ################################################
 
-
-dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
-
+dir.create(out_folder, recursive = T, showWarnings = F)
 
 ################################################
 #### Write table to file
 ################################################
 
-write.table(isa_merged, file = paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
+write.table(isa_merged, file = paste(out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
diff --git a/workflows/merge_isa_metadata.cwl b/workflows/merge_isa_metadata/workflow.cwl
similarity index 60%
rename from workflows/merge_isa_metadata.cwl
rename to workflows/merge_isa_metadata/workflow.cwl
index d812914728833fca5140a2b9347c5e6994aa52ce..19d1359295ab3181cb2ea4cf96b95ab720bd8d0b 100644
--- a/workflows/merge_isa_metadata.cwl
+++ b/workflows/merge_isa_metadata/workflow.cwl
@@ -2,28 +2,32 @@
 
 cwlVersion: v1.2
 class: CommandLineTool
-
+hints:
+  DockerRequirement:
+    dockerPull: zimmera95/rnaseq:latest
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - class: File
+        location: merge_isa_metadata.R
+baseCommand:
+- Rscript
+arguments:
+  - position: 0
+    valueFrom: merge_isa_metadata.R
 inputs:
-- id: r_script
+- id: in_isa_study
   type: File
-  inputBinding:
-    position: 0
-- id: arc_root
-  type: string
   inputBinding:
     position: 1
-- id: in_isa_study
-  type: string
-  inputBinding:
-    position: 2
 - id: in_isa_assay
-  type: string
+  type: File
   inputBinding:
-    position: 3
+    position: 2
 - id: out_folder
   type: string
   inputBinding:
-    position: 4
+    position: 3
 
 outputs:
 - id: outdir
@@ -32,6 +36,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
diff --git a/workflows/shiny_plots.Rmd b/workflows/shiny_prep/shiny_plots.Rmd
similarity index 100%
rename from workflows/shiny_plots.Rmd
rename to workflows/shiny_prep/shiny_plots.Rmd
diff --git a/workflows/shiny_prep.R b/workflows/shiny_prep/shiny_prep.R
similarity index 68%
rename from workflows/shiny_prep.R
rename to workflows/shiny_prep/shiny_prep.R
index a44796250a409d286eb330862a7cdb6c4b473036..07c44659bcacade29394ee895d9f9c38427e45bd 100644
--- a/workflows/shiny_prep.R
+++ b/workflows/shiny_prep/shiny_prep.R
@@ -4,7 +4,7 @@
 #### CWL-independent tests
 ################################################
 
-# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq/"
+# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq_adrian/"
 # out_folder <- "runs/shiny_prep"
 # in_kallisto_df <- "runs/kallisto_collect/kallisto_df.csv"
 
@@ -20,22 +20,21 @@
 
 args <- commandArgs(trailingOnly = T)
 
-arc_root <- args[1]
-out_folder <- args[2]
-in_kallisto_df <- args[3]
+out_folder <- args[1]
+in_kallisto_df <- args[2]
 
 ################################################
 #### If it does not exist, create out dir
 ################################################
 
-dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
+dir.create(out_folder, recursive = T, showWarnings = F)
 
 ################################################
 #### Prep data for shiny app
 ################################################
 
-expression_data <- read.csv(file = paste(arc_root, in_kallisto_df, sep = "/"))
+expression_data <- read.csv(file = in_kallisto_df)
 
 available_genes <- unique(expression_data$target_id)
 
-save(expression_data, available_genes, file = paste(arc_root, out_folder, 'shiny_prep.RData', sep = "/"))
+save(expression_data, available_genes, file = paste(out_folder, 'shiny_prep.RData', sep = "/"))
diff --git a/workflows/shiny_prep.cwl b/workflows/shiny_prep/workflow.cwl
similarity index 58%
rename from workflows/shiny_prep.cwl
rename to workflows/shiny_prep/workflow.cwl
index 918aaa0aefa401caed518703a64ac7fd6c333e3b..0e059d4968947b2f925c583b15b17e96d929a02d 100644
--- a/workflows/shiny_prep.cwl
+++ b/workflows/shiny_prep/workflow.cwl
@@ -1,26 +1,28 @@
 #!/usr/bin/env cwl-runner
-
 cwlVersion: v1.2
 class: CommandLineTool
-
+hints:
+  DockerRequirement:
+    dockerPull: zimmera95/rnaseq:latest
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - class: File
+        location: shiny_prep.R
+baseCommand:
+- Rscript
+arguments:
+  - position: 0
+    valueFrom: shiny_prep.R
 inputs:
-- id: r_script
-  type: File
-  inputBinding:
-    position: 0
-- id: arc_root
-  type: string
-  inputBinding:
-    position: 1
 - id: out_folder
   type: string
   inputBinding:
-    position: 2
+    position: 1
 - id: in_kallisto_df
-  type: string
+  type: File
   inputBinding:
-    position: 3
-
+    position: 2
 outputs:
 - id: outdir
   type:
@@ -28,6 +30,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
\ No newline at end of file