From e92c35867c7d9fc2184b9d66ef06386dc536ba42 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 2 Aug 2024 13:15:05 +0200
Subject: [PATCH] design workflow
---
runs/kallisto/README.md | 5 +++--
runs/kallisto/workflow.yml | 17 +++++++++-----
workflows/kallisto/kallisto-workflow.cwl | 28 +++++++++++++++++++-----
3 files changed, 36 insertions(+), 14 deletions(-)
diff --git a/runs/kallisto/README.md b/runs/kallisto/README.md
index f3a9d64..65d21cd 100644
--- a/runs/kallisto/README.md
+++ b/runs/kallisto/README.md
@@ -4,5 +4,6 @@
```bash
cd runs/kallisto/
-cwltool ../../workflows/kallisto/kallisto-index.cwl index.yml
-```
\ No newline at end of file
+cwltool --cachedir cache2 ../../workflows/kallisto/kallisto-workflow.cwl workflow.yml > $(date +"%Y-%m-%d_%H-%M").log 2>&1 &
+```
+
diff --git a/runs/kallisto/workflow.yml b/runs/kallisto/workflow.yml
index b21cbe8..e1d32d5 100644
--- a/runs/kallisto/workflow.yml
+++ b/runs/kallisto/workflow.yml
@@ -1,10 +1,15 @@
-InputReads:
+InputReadsMultipleSamples:
+ -
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
+ format: edam:format_1930 # FASTQ
+ -
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
+ format: edam:format_1930 # FASTQ
+IndexInput:
- class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
- format: edam:format_1930 # FASTQ
-InputFiles:
- - class: File
- path: ../../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
+ path: ../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
format: edam:format_1929 # FASTA
isSingle: true
FragmentLength: 200
diff --git a/workflows/kallisto/kallisto-workflow.cwl b/workflows/kallisto/kallisto-workflow.cwl
index 08047cd..37fb7df 100644
--- a/workflows/kallisto/kallisto-workflow.cwl
+++ b/workflows/kallisto/kallisto-workflow.cwl
@@ -3,25 +3,41 @@ class: Workflow
requirements:
ScatterFeatureRequirement: {}
+ StepInputExpressionRequirement: {}
+ InlineJavascriptRequirement: {}
inputs:
- InputReads: []
- Index: File
+ InputReadsMultipleSamples:
+ type:
+ type: array
+ items:
+ type: array
+ items: File
+ IndexInput: File[]
isSingle: boolean
FragmentLength: double?
StandardDeviation: double?
BootstrapSamples: int?
steps:
+ index:
+ run: kallisto-index.cwl
+ in:
+ InputFiles: IndexInput
+ IndexName:
+ source: IndexInput
+ valueFrom: $(self[0].nameroot)
+ out: [index]
quant:
run: kallisto-quant.cwl
scatter: InputReads
in:
- InputReads: listFiles/inDirFiles
+ InputReads: InputReadsMultipleSamples
QuantOutfolder:
- source: InputReads
- valueFrom: $(self.nameroot)
- Index: Index
+ # source: InputReadsMultipleSamples
+ # valueFrom: $(self[0].nameroot)
+ valueFrom: testSample
+ Index: index/index
isSingle: isSingle
FragmentLength: FragmentLength
StandardDeviation: StandardDeviation
--
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