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Commit 163979ff authored by Dominik Brilhaus's avatar Dominik Brilhaus
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remove old scripts, cwl approaches, run results

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#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
inputs:
- id: sh_script
type: File
inputBinding:
position: 0
- id: in_genome_ref
type: File
inputBinding:
position: 2
- id: out_folder
type: string
inputBinding:
position: 3
outputs:
- id: outdir
type:
type: array
items: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.out_folder)
baseCommand:
- bash
File deleted
{
"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": "0.48.0",
"index_version": 10,
"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"
}
File deleted
{
"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": "0.48.0",
"index_version": 10,
"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"
}
File deleted
{
"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": "0.48.0",
"index_version": 10,
"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"
}
File deleted
{
"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": "0.48.0",
"index_version": 10,
"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"
}
File deleted
{
"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": "0.48.0",
"index_version": 10,
"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"
}
File deleted
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