From 14e17ca67269deebf4f02dbc75b3267551907cc8 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Sat, 13 Aug 2022 16:26:41 +0200
Subject: [PATCH] Dockerize merge_isa_metadata

---
 runs/merged_isa_metadata/README.md            | 11 +------
 .../merge_isa_metadata.yml                    | 12 ++++----
 .../{ => out}/merged_isa.tsv                  | 12 ++++----
 runs/merged_isa_metadata/run.cwl              | 24 +++++++++++++++
 .../merge_isa_metadata/merge_isa_metadata.R   | 19 ++++++------
 workflows/merge_isa_metadata/workflow.cwl     | 30 ++++++++++---------
 6 files changed, 62 insertions(+), 46 deletions(-)
 rename runs/merged_isa_metadata/{ => out}/merged_isa.tsv (62%)
 create mode 100644 runs/merged_isa_metadata/run.cwl

diff --git a/runs/merged_isa_metadata/README.md b/runs/merged_isa_metadata/README.md
index 59c24de..3f48961 100644
--- a/runs/merged_isa_metadata/README.md
+++ b/runs/merged_isa_metadata/README.md
@@ -9,15 +9,6 @@ cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/merged_isa_meta
 ## 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 --enable-dev 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 0a52d03..4e4d2a1 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
\ No newline at end of file
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 24bea10..166ac5e 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 0000000..978e240
--- /dev/null
+++ b/runs/merged_isa_metadata/run.cwl
@@ -0,0 +1,24 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2.0-dev1
+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/workflows/merge_isa_metadata/merge_isa_metadata.R b/workflows/merge_isa_metadata/merge_isa_metadata.R
index 5af105c..aa074b3 100644
--- a/workflows/merge_isa_metadata/merge_isa_metadata.R
+++ b/workflows/merge_isa_metadata/merge_isa_metadata.R
@@ -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/workflow.cwl b/workflows/merge_isa_metadata/workflow.cwl
index d812914..436cc7d 100644
--- a/workflows/merge_isa_metadata/workflow.cwl
+++ b/workflows/merge_isa_metadata/workflow.cwl
@@ -1,29 +1,31 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.2
+cwlVersion: v1.2.0-dev1
 class: CommandLineTool
-
+hints:
+  DockerRequirement:
+    dockerPull: zimmera95/rnaseq:latest
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - class: File
+        location: merge_isa_metadata.R
+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
-- 
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