add runs without kallisto_index

runs/run1/02_assay_data.csv

+"","Sample.Name","Source.Name.x","Characteristics.[Biological.replicate]","Characteristics.[Organism]","Characteristics.[Organism.part]","Characteristics.[watering.exposure]","Source.Name.y","Source.Name.x","Data.File.Name","Source.Name.y","sample","Group"
+"1","CAM_01","CAM_01","rep1","Talinum triangulare","Leaf","12 days drought","CAM_01","CAM_01","DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz","CAM_01","DB_097","CAM"
+"2","CAM_02","CAM_02","rep2","Talinum triangulare","Leaf","12 days drought","CAM_02","CAM_02","DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz","CAM_02","DB_099","CAM"
+"3","CAM_03","CAM_03","rep3","Talinum triangulare","Leaf","12 days drought","CAM_03","CAM_03","DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz","CAM_03","DB_103","CAM"
+"4","reC3_01","reC3_01","rep1","Talinum triangulare","Leaf","2 days rewatered","reC3_01","reC3_01","DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz","reC3_01","DB_161","reC3"
+"5","reC3_02","reC3_02","rep2","Talinum triangulare","Leaf","2 days rewatered","reC3_02","reC3_02","DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz","reC3_02","DB_163","reC3"
+"6","reC3_03","reC3_03","rep3","Talinum triangulare","Leaf","2 days rewatered","reC3_03","reC3_03","DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz","reC3_03","DB_165","reC3"

runs/run1/03_kallisto_mappingStats.csv

+"ID","n_targets","n_bootstraps","n_processed","n_pseudoaligned","n_unique","p_pseudoaligned","p_unique","kallisto_version","index_version","start_time","call"
+"DB_097",31434,100,11071656,7663654,7522185,69.2,67.9,"0.44.0",10,"Fri Aug  6 15:48:13 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_097 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz"
+"DB_099",31434,100,14332278,10066506,9848811,70.2,68.7,"0.44.0",10,"Fri Aug  6 15:49:19 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_099 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz"
+"DB_103",31434,100,13083957,9007720,8828236,68.8,67.5,"0.44.0",10,"Fri Aug  6 15:50:41 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_103 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz"
+"DB_161",31434,100,12785081,9058396,8740183,70.9,68.4,"0.44.0",10,"Fri Aug  6 15:51:58 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_161 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz"
+"DB_163",31434,100,14312514,10054493,9707941,70.2,67.8,"0.44.0",10,"Fri Aug  6 15:53:12 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_163 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz"
+"DB_165",31434,100,13679479,9552504,9264346,69.8,67.7,"0.44.0",10,"Fri Aug  6 15:54:35 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_165 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz"

workflows/01_KallistoQuant.sh

@@ -3,7 +3,7 @@
 #### To be replaced by CWL routine
 ########################
 
-ARC_root=~/Hackathon_ARCexample_rnaseq/
+ARC_root=~/samplearc_rnaseq/
 cd $ARC_root'workflows/'
 
 # chmod a+x 01_KallistoQuant.sh