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Commit ddb74b10 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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cwl: merge isa metadata

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runs/merged_isa_metadata/merged_isa.tsv 0 → 100644
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"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"
workflows/merge_isa_metadata.R 0 → 100644
+ 91
− 0
View file @ ddb74b10
#!/usr/bin/env Rscript
################################################
#### Test area
################################################
# arc_root <- "~/03_DataPLANT_gitlab/samplearc_rnaseq/"
# in_isa_study <- "studies/TalinumFacultativeCAM/isa.study.xlsx:plant_growth"
# in_isa_assay <- "assays/Talinum_RNASeq_minimal/isa.assay.xlsx:2EXT01_RNA:3ASY01_RNASeq"
# out_folder <- "runs/merged_isa_metadata"
################################################
#### Load required library
################################################
library(openxlsx)
# library(tidyverse)
################################################
#### Read arguments from CLI
################################################
args <- commandArgs(trailingOnly = T)
arc_root <- args[1]
in_isa_study <- args[2]
in_isa_assay <- args[3]
out_folder <- args[4]
# setwd(arc_root)
################################################
#### 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_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)
})]
################################################
#### Write to file
################################################
## Create directory
dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
# dir.create(out_folder, recursive = T, showWarnings = F)
## Write
write.table(isa_merged, file = paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
# View(read.csv(paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t"))
workflows/merge_isa_metadata.cwl 0 → 100644
+ 37
− 0
View file @ ddb74b10
#!/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_isa_study
type: string
inputBinding:
position: 2
- id: in_isa_assay
type: string
inputBinding:
position: 3
- id: out_folder
type: string
inputBinding:
position: 4
outputs:
- id: outdir
type:
type: array
items: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.out_folder)
baseCommand:
- Rscript
workflows/merge_isa_metadata.yml 0 → 100644
+ 8
− 0
View file @ ddb74b10
cores: 1
r_script:
class: File
path: ./merge_isa_metadata.R
arc_root: /Users/dominikbrilhaus/03_DataPLANT_gitlab/samplearc_rnaseq/
in_isa_study: studies/TalinumFacultativeCAM/isa.study.xlsx:plant_growth
in_isa_assay: assays/Talinum_RNASeq_minimal/isa.assay.xlsx:2EXT01_RNA:3ASY01_RNASeq
out_folder: runs/merged_isa_metadata
\ No newline at end of file
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