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Commit a528bd08 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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cwl-run kallisto_quant and kallisto_sleuth

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......@@ -16,6 +16,6 @@ arc_root=$(echo ${PWD%/*/*})
sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_quant.yml
### run with cwltool
cwltool ../../workflows/kallisto_quant.cwl kallisto_index.yml
cwltool ../../workflows/kallisto_quant.cwl kallisto_quant.yml
```
{
"n_targets": 31434,
"n_bootstraps": 100,
"n_processed": 11071656,
"n_pseudoaligned": 7663654,
"n_unique": 7522185,
"p_pseudoaligned": 69.2,
"p_unique": 67.9,
"kallisto_version": "0.44.0",
"index_version": 10,
"start_time": "Fri Aug 6 15:48:13 2021",
"call": "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"
}
......@@ -8,6 +8,6 @@
"p_unique": 67.9,
"kallisto_version": "0.48.0",
"index_version": 10,
"start_time": "Wed Aug 10 17:20:19 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results_v48_anaconda/DB_097_CAMMD_CAGATC_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz"
"start_time": "Wed Aug 10 18:21:29 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz"
}
{
"n_targets": 31434,
"n_bootstraps": 100,
"n_processed": 14332278,
"n_pseudoaligned": 10066506,
"n_unique": 9848811,
"p_pseudoaligned": 70.2,
"p_unique": 68.7,
"kallisto_version": "0.44.0",
"index_version": 10,
"start_time": "Fri Aug 6 15:49:19 2021",
"call": "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"
}
......@@ -8,6 +8,6 @@
"p_unique": 68.7,
"kallisto_version": "0.48.0",
"index_version": 10,
"start_time": "Wed Aug 10 17:21:25 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results_v48_anaconda/DB_099_CAMMD_CTTGTA_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz"
"start_time": "Wed Aug 10 18:22:23 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz"
}
{
"n_targets": 31434,
"n_bootstraps": 100,
"n_processed": 13083957,
"n_pseudoaligned": 9007720,
"n_unique": 8828236,
"p_pseudoaligned": 68.8,
"p_unique": 67.5,
"kallisto_version": "0.44.0",
"index_version": 10,
"start_time": "Fri Aug 6 15:50:41 2021",
"call": "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"
}
......@@ -8,6 +8,6 @@
"p_unique": 67.5,
"kallisto_version": "0.48.0",
"index_version": 10,
"start_time": "Wed Aug 10 17:22:51 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results_v48_anaconda/DB_103_CAMMD_AGTCAA_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz"
"start_time": "Wed Aug 10 18:23:36 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz"
}
{
"n_targets": 31434,
"n_bootstraps": 100,
"n_processed": 12785081,
"n_pseudoaligned": 9058396,
"n_unique": 8740183,
"p_pseudoaligned": 70.9,
"p_unique": 68.4,
"kallisto_version": "0.44.0",
"index_version": 10,
"start_time": "Fri Aug 6 15:51:58 2021",
"call": "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"
}
......@@ -8,6 +8,6 @@
"p_unique": 68.4,
"kallisto_version": "0.48.0",
"index_version": 10,
"start_time": "Wed Aug 10 17:24:22 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results_v48_anaconda/DB_161_reC3MD_GTCCGC_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz"
"start_time": "Wed Aug 10 18:24:45 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz"
}
{
"n_targets": 31434,
"n_bootstraps": 100,
"n_processed": 14312514,
"n_pseudoaligned": 10054493,
"n_unique": 9707941,
"p_pseudoaligned": 70.2,
"p_unique": 67.8,
"kallisto_version": "0.44.0",
"index_version": 10,
"start_time": "Fri Aug 6 15:53:12 2021",
"call": "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"
}
......@@ -8,6 +8,6 @@
"p_unique": 67.8,
"kallisto_version": "0.48.0",
"index_version": 10,
"start_time": "Wed Aug 10 17:25:43 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results_v48_anaconda/DB_163_reC3MD_GTGAAA_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz"
"start_time": "Wed Aug 10 18:25:50 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz"
}
{
"n_targets": 31434,
"n_bootstraps": 100,
"n_processed": 13679479,
"n_pseudoaligned": 9552504,
"n_unique": 9264346,
"p_pseudoaligned": 69.8,
"p_unique": 67.7,
"kallisto_version": "0.44.0",
"index_version": 10,
"start_time": "Fri Aug 6 15:54:35 2021",
"call": "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"
}
......@@ -8,6 +8,6 @@
"p_unique": 67.7,
"kallisto_version": "0.48.0",
"index_version": 10,
"start_time": "Wed Aug 10 17:27:10 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results_v48_anaconda/DB_165_re-C3MD_GTGAAA_L002_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz"
"start_time": "Wed Aug 10 18:26:59 2022",
"call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz"
}
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