diff --git a/runs/merged_isa_metadata/out/merged_isa.tsv b/runs/merged_isa_metadata/out/merged_isa.tsv
deleted file mode 100644
index 24bea101e89b855a18d5d294556d6d0f0ca4f170..0000000000000000000000000000000000000000
--- a/runs/merged_isa_metadata/out/merged_isa.tsv
+++ /dev/null
@@ -1,7 +0,0 @@
-"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"
diff --git a/runs/merged_isa_metadata/run.cwl b/runs/merged_isa_metadata/run.cwl
deleted file mode 100644
index 859ac0b1c11de8981a582ea4bc1b12526c12c909..0000000000000000000000000000000000000000
--- a/runs/merged_isa_metadata/run.cwl
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env cwl-runner
-cwlVersion: v1.2
-class: CommandLineTool
-inputs:
-- id: r_script
-  type: File
-  inputBinding:
-    position: 0
-- id: in_isa_study
-  type: File
-  inputBinding:
-    position: 1
-- id: in_isa_assay
-  type: File
-  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/runs/merged_isa_metadata/run.yml b/runs/merged_isa_metadata/run.yml
deleted file mode 100644
index 154dc89bd42c3a389aecb4a80ad8d3d868d167d4..0000000000000000000000000000000000000000
--- a/runs/merged_isa_metadata/run.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-cores: 1
-r_script:
-  class: File
-  path: ../../workflows/merge_isa_metadata/merge_isa_metadata.R
-in_isa_study: 
-  class: 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/workflows/deseq2/README.md b/workflows/deseq2/README.md
index 4a64681c020e2dd6d7da19503fc7c82f39896bce..8b68f05954783ac9a6cc39c9861dadd38b90d05f 100644
--- a/workflows/deseq2/README.md
+++ b/workflows/deseq2/README.md
@@ -28,13 +28,6 @@ BiocManager::install("rhdf5")
 library("rhdf5")
 ```
 
-### test
-
-```bash
-RScript deseq2.R "../../runs/kallisto/kallisto_results" "../../runs/merged_isa_metadata/out/merged_isa.tsv" "Source.Name" "Factor..Photosynthesis.mode."
-```
-
-
 ## Multi-package containers
 
 - R and combinations of library dependencies are available as multi-package containers from [BioContainers](https://github.com/BioContainers/multi-package-containers)
diff --git a/workflows/merge_isa_metadata/merge_isa_metadata.R b/workflows/merge_isa_metadata/merge_isa_metadata.R
deleted file mode 100644
index b4daca150962998854d9a3aaaf7d3f695a98b524..0000000000000000000000000000000000000000
--- a/workflows/merge_isa_metadata/merge_isa_metadata.R
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/usr/bin/env Rscript
-
-################################################
-#### Load required library
-################################################
-
-library(openxlsx)
-
-################################################
-#### Read arguments from CLI
-################################################
-
-args <- commandArgs(trailingOnly = T)
-
-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(in_isa_study, split = ":"))
-isa_assay <- unlist(strsplit(in_isa_assay, split = ":"))
-
-isa_sheets <- list()
-for (i in 2:length(isa_study))
-{
-  isa_sheets[[length(isa_sheets) + 1]] <- readWorkbook(isa_study[1], isa_study[i], startRow = 1)
-}
-
-for (i in 2:length(isa_assay))
-{
-  isa_sheets[[length(isa_sheets) + 1]] <- readWorkbook(isa_assay[1], isa_assay[i], startRow = 1)
-}
-
-################################################
-#### Merge consecutively right (Source.Name) to left (Sample.Name)
-################################################
-
-isa_merged <- isa_sheets[[1]]
-
-for (j in 2:length(isa_sheets))
-# for(j in 2)
-{
-  isa_merged <- merge(isa_merged,
-    isa_sheets[[j]],
-    by.x = "Sample.Name",
-    by.y = "Source.Name",
-  )
-
-  # Rename duplicated Sample.Name column
-
-  colnames(isa_merged)[which(colnames(isa_merged) == "Sample.Name")] <- paste("Sample.Name", j, sep = ".")
-  colnames(isa_merged)[which(colnames(isa_merged) == "Sample.Name.y")] <- "Sample.Name"
-}
-
-
-## remove empty columns
-isa_merged <- isa_merged[, !apply(isa_merged, 2, function(x) {
-  sum(is.na(x)) == nrow(isa_merged)
-})]
-
-
-################################################
-#### If it does not exist, create out dir
-################################################
-
-dir.create(out_folder, recursive = T, showWarnings = F)
-
-################################################
-#### Write table to file
-################################################
-
-write.table(isa_merged, file = paste(out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")