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Commit be46d9df authored by Dominik Brilhaus's avatar Dominik Brilhaus
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align with spec: isaSampleToRawData

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1 merge request!11Restructure cwl
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runs/isaSampleToRawDataSeq-run/README.md deleted 100644 → 0
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```bash
cd runs/isaSampleToRawDataSeq-run
```
```bash
cwltool ../../workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl job.yml
```
runs/isaSampleToRawDataSeq-run/rnaseq-samples.xlsx deleted 100644 → 0
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File deleted
runs/isaSampleToRawDataSeq-run/rnaseq-samples.csv → runs/isaSampleToRawDataSeq/rnaseq-samples.csv
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− 7
View file @ be46d9df
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]
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
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
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
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
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
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
\ No newline at end of file
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
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,,
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,,
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,,
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,,
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,,
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,,
\ No newline at end of file
runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx 0 → 100644
+ 0
− 0
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File added
runs/isaSampleToRawDataSeq/run.cwl 0 → 100644
+ 24
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cwlVersion: v1.2
class: Workflow
inputs:
arcPath: Directory
assayName: string
startingNodeNum: int
outName: string
steps:
isaSampleToRawDataSeq:
run: ../../workflows/isaSampleToRawDataSeq/workflow.cwl
in:
arcPath: arcPath
assayName: assayName
startingNodeNum: startingNodeNum
outName: outName
out: [output]
outputs:
output:
type: File[]
outputSource: isaSampleToRawDataSeq/output
workflows/isaSampleToRawDataSeq/README.md deleted 100644 → 0
+ 0
− 7
View file @ 7aa6183e
```bash
dotnet fsi isaSampleToRawDataSeq.fsx ../../ Talinum_RNASeq_minimal 1 rnaseq-samples
```
workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl → workflows/isaSampleToRawDataSeq/workflow.cwl
+ 4
− 0
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cwlVersion: v1.2
class: CommandLineTool
doc: |
Run script with `dotnet fsi isaSampleToRawDataSeq.fsx ../../ Talinum_RNASeq_minimal 1 rnaseq-samples`
hints:
DockerRequirement:
dockerPull: mcr.microsoft.com/dotnet/sdk:8.0
......
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