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Commit 26181b2f authored by Dominik Brilhaus's avatar Dominik Brilhaus
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adapt isaSampleToRawDataSeq to start from Source (not Sample)

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1 merge request!11Restructure cwl
Pipeline #9300 passed
Stage: arc_json
    Stage: quality_report_generator
      Stage: quality_report
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        runs/isaSampleToRawDataSeq/rnaseq-samples.csv
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        View file @ 26181b2f
        Input [Sample Name],Characteristic [organism],Term Source REF (OBI:0100026),Term Accession Number (OBI:0100026),Characteristic [organism part],Term Source REF (EFO:0000635),Term Accession Number (EFO:0000635),Characteristic [plant age],Term Source REF (DPBO:0000033),Term Accession Number (DPBO:0000033),Parameter [growth day length],Term Source REF (DPBO:0000041),Term Accession Number (DPBO:0000041),Parameter [light intensity exposure],Unit,Term Source REF (PECO:0007224),Term Accession Number (PECO:0007224),Parameter [humidity day],Unit ,Term Source REF (DPBO:0000005),Term Accession Number (DPBO:0000005),Parameter [temperature day],Unit ,Term Source REF (DPBO:0000007),Term Accession Number (DPBO:0000007),Parameter [temperature night],Unit ,Term Source REF (DPBO:0000008),Term Accession Number (DPBO:0000008),Factor [watering exposure],Term Source REF (PECO:0007383),Term Accession Number (PECO:0007383),Factor [Timepoint],Term Source REF (NCIT:C68568),Term Accession Number (NCIT:C68568),Factor [timepoint-ZT],Term Source REF (),Term Accession Number (),Factor [Photosynthesis mode],Term Source REF () ,Term Accession Number () ,Parameter [biosource amount],Unit ,Term Source REF (DPBO:0000013),Term Accession Number (DPBO:0000013),Parameter [extraction method],Term Source REF (DPBO:0000054),Term Accession Number (DPBO:0000054),Parameter [extraction buffer],Term Source REF (DPBO:0000050),Term Accession Number (DPBO:0000050),Parameter [extraction buffer volume],Unit ,Term Source REF (DPBO:0000051),Term Accession Number (DPBO:0000051),Parameter [RNA quality check],Term Source REF (DPBO:0000062),Term Accession Number (DPBO:0000062),Parameter [library strategy],Term Source REF (DPBO:0000035),Term Accession Number (DPBO:0000035),Parameter [library selection],Term Source REF (DPBO:0000036),Term Accession Number (DPBO:0000036),Parameter [library layout],Term Source REF (DPBO:0000015),Term Accession Number (DPBO:0000015),Parameter [library preparation kit],Term Source REF (GENEPIO:0000085),Term Accession Number (GENEPIO:0000085),Parameter [library preparation kit version],Term Source REF (GENEPIO:0000149),Term Accession Number (GENEPIO:0000149),Parameter [adapter sequence],Term Source REF (GENEPIO:0000083),Term Accession Number (GENEPIO:0000083),Parameter [next generation sequencing instrument model],Term Source REF (DPBO:0000040),Term Accession Number (DPBO:0000040),Parameter [base-calling software],Term Source REF (DPBO:0000017),Term Accession Number (DPBO:0000017),Parameter [base-calling software version],Term Source REF (DPBO:0000018),Term Accession Number (DPBO:0000018),Parameter [Raw data file format],Term Source REF (DPBO:0000021),Term Accession Number (DPBO:0000021),Output [Data],Data Format,Data Selector Format Input [Source Name],Characteristic [organism],Term Source REF (OBI:0100026),Term Accession Number (OBI:0100026),Characteristic [organism part],Term Source REF (EFO:0000635),Term Accession Number (EFO:0000635),Characteristic [plant age],Term Source REF (DPBO:0000033),Term Accession Number (DPBO:0000033),Parameter [growth day length],Term Source REF (DPBO:0000041),Term Accession Number (DPBO:0000041),Parameter [light intensity exposure],Unit,Term Source REF (PECO:0007224),Term Accession Number (PECO:0007224),Parameter [humidity day],Unit ,Term Source REF (DPBO:0000005),Term Accession Number (DPBO:0000005),Parameter [temperature day],Unit ,Term Source REF (DPBO:0000007),Term Accession Number (DPBO:0000007),Parameter [temperature night],Unit ,Term Source REF (DPBO:0000008),Term Accession Number (DPBO:0000008),Factor [watering exposure],Term Source REF (PECO:0007383),Term Accession Number (PECO:0007383),Factor [Timepoint],Term Source REF (NCIT:C68568),Term Accession Number (NCIT:C68568),Factor [timepoint-ZT],Term Source REF (),Term Accession Number (),Factor [Photosynthesis mode],Term Source REF () ,Term Accession Number () ,Parameter [biosource amount],Unit ,Term Source REF (DPBO:0000013),Term Accession Number (DPBO:0000013),Parameter [extraction method],Term Source REF (DPBO:0000054),Term Accession Number (DPBO:0000054),Parameter [extraction buffer],Term Source REF (DPBO:0000050),Term Accession Number (DPBO:0000050),Parameter [extraction buffer volume],Unit ,Term Source REF (DPBO:0000051),Term Accession Number (DPBO:0000051),Parameter [RNA quality check],Term Source REF (DPBO:0000062),Term Accession Number (DPBO:0000062),Parameter [library strategy],Term Source REF (DPBO:0000035),Term Accession Number (DPBO:0000035),Parameter [library selection],Term Source REF (DPBO:0000036),Term Accession Number (DPBO:0000036),Parameter [library layout],Term Source REF (DPBO:0000015),Term Accession Number (DPBO:0000015),Parameter [library preparation kit],Term Source REF (GENEPIO:0000085),Term Accession Number (GENEPIO:0000085),Parameter [library preparation kit version],Term Source REF (GENEPIO:0000149),Term Accession Number (GENEPIO:0000149),Parameter [adapter sequence],Term Source REF (GENEPIO:0000083),Term Accession Number (GENEPIO:0000083),Parameter [next generation sequencing instrument model],Term Source REF (DPBO:0000040),Term Accession Number (DPBO:0000040),Parameter [base-calling software],Term Source REF (DPBO:0000017),Term Accession Number (DPBO:0000017),Parameter [base-calling software version],Term Source REF (DPBO:0000018),Term Accession Number (DPBO:0000018),Parameter [Raw data file format],Term Source REF (DPBO:0000021),Term Accession Number (DPBO:0000021),Output [Data],Data Format,Data Selector Format
        CAM_01,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought,user-specific,,MD,user-specific,,6,user-specific,,CAM,user-specific,,80,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,CAGATC,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz,, DB_097,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought,user-specific,,MD,user-specific,,6,user-specific,,CAM,user-specific,,80,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,CAGATC,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz,,
        CAM_02,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought,user-specific,,MD,user-specific,,6,user-specific,,CAM,user-specific,,78,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.7 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,CTTGTA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz,, DB_099,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought,user-specific,,MD,user-specific,,6,user-specific,,CAM,user-specific,,78,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.7 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,CTTGTA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz,,
        CAM_03,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought,user-specific,,MD,user-specific,,6,user-specific,,CAM,user-specific,,93,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 6.5 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,AGTCAA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz,, DB_103,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought,user-specific,,MD,user-specific,,6,user-specific,,CAM,user-specific,,93,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 6.5 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,AGTCAA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz,,
        reC3_01,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought + 2 days rewatered,user-specific,,MD,user-specific,,6,user-specific,,reC3,user-specific,,82,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.8 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,GTCCGC,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz,, DB_161,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought + 2 days rewatered,user-specific,,MD,user-specific,,6,user-specific,,reC3,user-specific,,82,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.8 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,GTCCGC,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz,,
        reC3_02,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought + 2 days rewatered,user-specific,,MD,user-specific,,6,user-specific,,reC3,user-specific,,96,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,GTGAAA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz,, DB_163,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought + 2 days rewatered,user-specific,,MD,user-specific,,6,user-specific,,reC3,user-specific,,96,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,GTGAAA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz,,
        reC3_03,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought + 2 days rewatered,user-specific,,MD,user-specific,,6,user-specific,,reC3,user-specific,,78,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,GTGAAA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz,, DB_165,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought + 2 days rewatered,user-specific,,MD,user-specific,,6,user-specific,,reC3,user-specific,,78,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,GTGAAA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz,,
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        View file @ 26181b2f
        ...@@ -2,17 +2,25 @@ ...@@ -2,17 +2,25 @@
        // Dependencies // Dependencies
        #r "nuget: ARCtrl.NET" #r "nuget: ARCtrl"
        #r "nuget: ARCtrl.QueryModel" #r "nuget: ARCtrl.QueryModel"
        #r "nuget: FsSpreadsheet.CsvIO" #r "nuget: FsSpreadsheet.CsvIO"
        open ARCtrl.NET
        open ARCtrl open ARCtrl
        open ARCtrl.QueryModel open ARCtrl.QueryModel
        open ARCtrl.Helper open ARCtrl.Helper
        open FsSpreadsheet.Net open FsSpreadsheet.Net
        open FsSpreadsheet.CsvIO open FsSpreadsheet.CsvIO
        // test parameters
        // let source = __SOURCE_DIRECTORY__
        // let arcPath = System.IO.Path.Combine(source, "../../")
        // let assayName = "Talinum_RNASeq_minimal"
        // let startingNodeNum = 0
        // let outName = "rnaseq-samples"
        // input parameters // input parameters
        let args : string array = fsi.CommandLineArgs |> Array.tail let args : string array = fsi.CommandLineArgs |> Array.tail
        ...@@ -31,13 +39,6 @@ type ArcTables with ...@@ -31,13 +39,6 @@ type ArcTables with
        ) )
        |> ArcTables |> ArcTables
        // // test parameters
        // let source = __SOURCE_DIRECTORY__
        // let arcPath = Path.Combine(source, "../../")
        // let assayName = "Talinum_RNASeq_minimal"
        // let startingNodeNum = 0
        // let outName = "rnaseq-samples"
        // Load ARC // Load ARC
        // Remove all tables with either an input or output column missing // Remove all tables with either an input or output column missing
        ...@@ -97,8 +98,6 @@ let shittify (a : ARC) = ...@@ -97,8 +98,6 @@ let shittify (a : ARC) =
        let arc = ARC.load(arcPath) |> clean |> shittify let arc = ARC.load(arcPath) |> clean |> shittify
        let inv = arc.ISA.Value let inv = arc.ISA.Value
        // Load first data node // Load first data node
        ...@@ -108,7 +107,11 @@ let firstData = inv.GetAssay(assayName).FirstData ...@@ -108,7 +107,11 @@ let firstData = inv.GetAssay(assayName).FirstData
        // Create headers for output table // Create headers for output table
        let headers = [ let headers = [
        CompositeHeader.Input IOType.Sample
        CompositeHeader.Input IOType.Source
        // CompositeHeader.Input IOType.Sample
        for v in inv.ArcTables.IgnoreShitty().ValuesOf firstData.[0].Name do for v in inv.ArcTables.IgnoreShitty().ValuesOf firstData.[0].Name do
        if v.IsCharacteristicValue then if v.IsCharacteristicValue then
        CompositeHeader.Characteristic v.Category CompositeHeader.Characteristic v.Category
        ...@@ -128,7 +131,7 @@ let headers = [ ...@@ -128,7 +131,7 @@ let headers = [
        let getRow (d: QNode) = let getRow (d: QNode) =
        [| [|
        CompositeCell.createFreeText (inv.ArcTables.SamplesOf d).[startingNodeNum].Name CompositeCell.createFreeText (inv.ArcTables.SourcesOf d).[startingNodeNum].Name
        for v in inv.ArcTables.ValuesOf d do for v in inv.ArcTables.ValuesOf d do
        if v.HasUnit then if v.HasUnit then
        ...@@ -165,4 +168,4 @@ wb.AddWorksheet ws ...@@ -165,4 +168,4 @@ wb.AddWorksheet ws
        wb.ToXlsxFile ($"{outName}.xlsx") wb.ToXlsxFile ($"{outName}.xlsx")
        // Write to csv // Write to csv
        wb.ToCsvFile ($"{outName}.csv") wb.ToCsvFile ($"{outName}.csv")
        \ No newline at end of file
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