diff --git a/runs/isaSampleToRawDataSeq-run/README.md b/runs/isaSampleToRawDataSeq-run/README.md
deleted file mode 100644
index 6c83a17dc1ab439d90ae08c2749a9047ac74ba3f..0000000000000000000000000000000000000000
--- a/runs/isaSampleToRawDataSeq-run/README.md
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-
-```bash
-cd runs/isaSampleToRawDataSeq-run
-```
-
-```bash
-cwltool ../../workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl job.yml
-```
diff --git a/runs/isaSampleToRawDataSeq-run/rnaseq-samples.xlsx b/runs/isaSampleToRawDataSeq-run/rnaseq-samples.xlsx
deleted file mode 100644
index 759961513f5d109aacc26dcc233d07e5c0e1325f..0000000000000000000000000000000000000000
Binary files a/runs/isaSampleToRawDataSeq-run/rnaseq-samples.xlsx and /dev/null differ
diff --git a/runs/isaSampleToRawDataSeq-run/rnaseq-samples.csv b/runs/isaSampleToRawDataSeq/rnaseq-samples.csv
similarity index 96%
rename from runs/isaSampleToRawDataSeq-run/rnaseq-samples.csv
rename to runs/isaSampleToRawDataSeq/rnaseq-samples.csv
index d9aed97c919b39486aa0d1ccea4319a46a00dd5e..94042890d63cbbc5fbd7ca3265ad1feeace15548 100644
--- a/runs/isaSampleToRawDataSeq-run/rnaseq-samples.csv
+++ b/runs/isaSampleToRawDataSeq/rnaseq-samples.csv
@@ -1,7 +1,7 @@
-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
diff --git a/runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx b/runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..7932354fc2ad69ab4f57f3cabfac0a7d9309c5b5
Binary files /dev/null and b/runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx differ
diff --git a/runs/isaSampleToRawDataSeq/run.cwl b/runs/isaSampleToRawDataSeq/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..8f00f6abfd1d3f757b20fdf253fbbcd0b0003aa5
--- /dev/null
+++ b/runs/isaSampleToRawDataSeq/run.cwl
@@ -0,0 +1,24 @@
+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
+
diff --git a/runs/isaSampleToRawDataSeq-run/job.yml b/runs/isaSampleToRawDataSeq/run.yml
similarity index 100%
rename from runs/isaSampleToRawDataSeq-run/job.yml
rename to runs/isaSampleToRawDataSeq/run.yml
diff --git a/workflows/isaSampleToRawDataSeq/README.md b/workflows/isaSampleToRawDataSeq/README.md
deleted file mode 100644
index 8ecbd0b4085a745e8261cee82c4a8116ed624667..0000000000000000000000000000000000000000
--- a/workflows/isaSampleToRawDataSeq/README.md
+++ /dev/null
@@ -1,7 +0,0 @@
-
-
-```bash
-
-dotnet fsi isaSampleToRawDataSeq.fsx ../../ Talinum_RNASeq_minimal 1 rnaseq-samples
-
-```
diff --git a/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl b/workflows/isaSampleToRawDataSeq/workflow.cwl
similarity index 88%
rename from workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl
rename to workflows/isaSampleToRawDataSeq/workflow.cwl
index e743f327893969785482e36b2ba868dde93de35a..c2ef89de0657e40149af4c0419e5e21076c92cc6 100644
--- a/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl
+++ b/workflows/isaSampleToRawDataSeq/workflow.cwl
@@ -1,5 +1,9 @@
 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