cleaning

runs/kallisto/single-steps/README.md

-# Kallisto
-
-## Executing individual steps
-
-### Create genome index
-
-```bash
-cwltool ../../../workflows/kallisto/kallisto-index.cwl index.yml
-
-```
-
-### Quantification of a single sample
-
-```bash
-cwltool ../../../workflows/kallisto/kallisto-quant.cwl quant.yml
-```

runs/kallisto/single-steps/index.yml

-InputFiles:
-  - class: File
-    path: ../../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
-    format: edam:format_1929 # FASTA
-IndexName: "Talinum.gm.CDS"
-
-$namespaces:
-  edam: https://edamontology.org/
\ No newline at end of file

runs/kallisto/single-steps/quant.yml

-InputReads: 
-  - class: File
-    path: ../../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
-    format: edam:format_1930 # FASTA
-QuantOutfolder: DB_097
-Index:
-  class: File
-  path: ./Talinum.gm.CDS.kallistoIndex
-isSingle: true
-FragmentLength: 200
-StandardDeviation: 20
-BootstrapSamples: 30
-
-$namespaces:
-  edam: https://edamontology.org/
\ No newline at end of file

workflows/deseq2/mutli-docker-test.cwl

-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.2
-class: CommandLineTool
-
-requirements:
-  - class: DockerRequirement
-    dockerPull: quay.io/biocontainers/mulled-v2-05fd88b9ac812a9149da2f2d881d62f01cc49835:a10f0e3a7a70fc45494f8781d33901086d2214d0-0
-
-baseCommand: [Rscript, --help]
-
-inputs: []
-
-outputs: []