From 988ac5061e569e0d70a612b54ea25528967cd1a4 Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus <brilhaus@nfdi4plants.org> Date: Mon, 17 Mar 2025 17:16:30 +0100 Subject: [PATCH] cleaning --- runs/kallisto/single-steps/README.md | 16 ---------------- runs/kallisto/single-steps/index.yml | 8 -------- runs/kallisto/single-steps/quant.yml | 15 --------------- studies/.gitkeep | 0 workflows/deseq2/mutli-docker-test.cwl | 14 -------------- 5 files changed, 53 deletions(-) delete mode 100644 runs/kallisto/single-steps/README.md delete mode 100644 runs/kallisto/single-steps/index.yml delete mode 100644 runs/kallisto/single-steps/quant.yml delete mode 100644 studies/.gitkeep delete mode 100644 workflows/deseq2/mutli-docker-test.cwl diff --git a/runs/kallisto/single-steps/README.md b/runs/kallisto/single-steps/README.md deleted file mode 100644 index 847851e..0000000 --- a/runs/kallisto/single-steps/README.md +++ /dev/null @@ -1,16 +0,0 @@ -# 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 -``` diff --git a/runs/kallisto/single-steps/index.yml b/runs/kallisto/single-steps/index.yml deleted file mode 100644 index 70501a1..0000000 --- a/runs/kallisto/single-steps/index.yml +++ /dev/null @@ -1,8 +0,0 @@ -InputFiles: - - class: File - path: ../../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa - format: edam:format_1929 # FASTA -IndexName: "Talinum.gm.CDS" - -$namespaces: - edam: https://edamontology.org/ \ No newline at end of file diff --git a/runs/kallisto/single-steps/quant.yml b/runs/kallisto/single-steps/quant.yml deleted file mode 100644 index bd6cb6a..0000000 --- a/runs/kallisto/single-steps/quant.yml +++ /dev/null @@ -1,15 +0,0 @@ -InputReads: - - class: File - path: ../../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz - format: edam:format_1930 # FASTA -QuantOutfolder: DB_097 -Index: - class: File - path: ./Talinum.gm.CDS.kallistoIndex -isSingle: true -FragmentLength: 200 -StandardDeviation: 20 -BootstrapSamples: 30 - -$namespaces: - edam: https://edamontology.org/ \ No newline at end of file diff --git a/studies/.gitkeep b/studies/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/workflows/deseq2/mutli-docker-test.cwl b/workflows/deseq2/mutli-docker-test.cwl deleted file mode 100644 index 136d87e..0000000 --- a/workflows/deseq2/mutli-docker-test.cwl +++ /dev/null @@ -1,14 +0,0 @@ -#!/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: [] -- GitLab