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Commit 960e623a authored by Dominik Brilhaus's avatar Dominik Brilhaus
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Merge branch 'cwl' into 'main'

Cwl

See merge request !1
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**/dataset/** filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/runs/kallisto_index/out/kallisto_index filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_55.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_03.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_15.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_55.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_55.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_15.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_12.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_16.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_11.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_55.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_61.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_11.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_11.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_14.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_03.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_13.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_11.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_12.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_13.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_13.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_65.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150112_61.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa filter=lfs diff=lfs merge=lfs -text
runs/run1/01_kallisto_results/DB_103/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results_v48_anaconda/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run1/03_kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run1/01_kallisto_results/DB_099/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results_v48_anaconda/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_103/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run1/01_kallisto_index filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_097/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run1/03_kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run2/03_kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_163/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/sleuth_dge.csv filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_13.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_14.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/MSPeak.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_15.D/AcqData/TDASpec.bin filter=lfs diff=lfs merge=lfs -text
/assays/GCqTOF_targets/dataset/150115_16.D/AcqData/TDA.bin filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
runs/kallisto_collect/kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results_v48_anaconda/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/run1/01_kallisto_results/DB_097/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/run1/01_kallisto_results/DB_161/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_161/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run1/01_kallisto_results/DB_103/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/run1/01_kallisto_index filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run1/01_kallisto_results/DB_163/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run2/03_kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_097/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run1/03_kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run1/01_kallisto_results/DB_161/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results_v48_anaconda/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/sleuth_dge.csv filter=lfs diff=lfs merge=lfs -text
studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa filter=lfs diff=lfs merge=lfs -text
runs/kallisto_collect/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
runs/run1/01_kallisto_results/DB_165/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_099/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_collect/out/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_103/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_165/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_results/DB_099/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results_v48_anaconda/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run1/01_kallisto_results/DB_097/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run2/03_kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
externals/Talinum.gm.CDS.nt.fa filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run1/03_kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run1/01_kallisto_results/DB_165/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_sleuth/run2/03_kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
runs/run1/01_kallisto_results/DB_099/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/run1/03_kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/run1/03_kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
runs/run1/01_kallisto_results/DB_163/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/kallisto_quant/kallisto_results_v48_anaconda/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5 filter=lfs diff=lfs merge=lfs -text
runs/no_CWL_yet/kallisto_sleuth/run1/01_kallisto_index filter=lfs diff=lfs merge=lfs -text
runs/kallisto/kallisto_results/** filter=lfs diff=lfs merge=lfs -text
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......@@ -386,3 +386,6 @@ Temporary Items
# R temporaries
.Rhistory
.RData
# CWL caches
**/cache*/
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File moved
# Kallisto Workflow
## Executing the multi-step workflow
```bash
cd runs/kallisto/
cwltool --cachedir cache2 ../../workflows/kallisto/kallisto-workflow.cwl workflow.yml > $(date +"%Y-%m-%d_%H-%M").log 2>&1 &
```
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