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: []
-- 
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