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Commit 62287362 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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rm deprecated isa merge

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1 merge request!12Restructure cwl
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Stage: arc_json
    Stage: quality_report_generator
      Stage: quality_report
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        runs/merged_isa_metadata/out/merged_isa.tsv deleted 100644 → 0
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        View file @ 77cbdcf9
        "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"
        runs/merged_isa_metadata/run.cwl deleted 100644 → 0
        + 0
        − 30
        View file @ 77cbdcf9
        #!/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
        runs/merged_isa_metadata/run.yml deleted 100644 → 0
        + 0
        − 11
        View file @ 77cbdcf9
        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
        workflows/deseq2/README.md
        + 0
        − 7
        View file @ 62287362
        ...@@ -28,13 +28,6 @@ BiocManager::install("rhdf5") ...@@ -28,13 +28,6 @@ BiocManager::install("rhdf5")
        library("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 ## Multi-package containers
        - R and combinations of library dependencies are available as multi-package containers from [BioContainers](https://github.com/BioContainers/multi-package-containers) - R and combinations of library dependencies are available as multi-package containers from [BioContainers](https://github.com/BioContainers/multi-package-containers)
        ......
        workflows/merge_isa_metadata/merge_isa_metadata.R deleted 100644 → 0
        + 0
        − 77
        View file @ 77cbdcf9
        #!/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")
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