From 693ee201fade909f419f951672c18848aa50bc5b Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 14 Mar 2025 10:55:50 +0100
Subject: [PATCH] align with spec: kallisto
---
runs/kallisto/README.md | 8 ----
runs/kallisto/run.cwl | 40 +++++++++++++++++++
runs/kallisto/{workflow.yml => run.yml} | 34 ++++++++--------
workflows/.gitkeep | 0
workflows/kallisto/kallisto-index.cwl | 2 +-
workflows/kallisto/kallisto-quant.cwl | 2 +-
.../{kallisto-workflow.cwl => workflow.cwl} | 0
7 files changed, 59 insertions(+), 27 deletions(-)
delete mode 100644 runs/kallisto/README.md
create mode 100644 runs/kallisto/run.cwl
rename runs/kallisto/{workflow.yml => run.yml} (56%)
delete mode 100644 workflows/.gitkeep
rename workflows/kallisto/{kallisto-workflow.cwl => workflow.cwl} (100%)
diff --git a/runs/kallisto/README.md b/runs/kallisto/README.md
deleted file mode 100644
index e3c73f3..0000000
--- a/runs/kallisto/README.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# Kallisto Workflow
-
-## Executing the multi-step workflow
-
-```bash
-cd runs/kallisto/
-cwltool --cachedir cache2 ../../workflows/kallisto/kallisto-workflow.cwl workflow.yml > $(date +"%Y-%m-%d_%H-%M").log 2>&1 &
-```
diff --git a/runs/kallisto/run.cwl b/runs/kallisto/run.cwl
new file mode 100644
index 0000000..7ab4d83
--- /dev/null
+++ b/runs/kallisto/run.cwl
@@ -0,0 +1,40 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+ SubworkflowFeatureRequirement: {}
+
+inputs:
+ IndexInput: File[]
+ InputReadsMultipleSamples:
+ type:
+ type: array
+ items:
+ type: array
+ items: File
+ numUnderscoresFileName: int
+ isSingle: boolean
+ FragmentLength: double?
+ StandardDeviation: double?
+ BootstrapSamples: int?
+ resultsFolder: string
+
+steps:
+ kallisto:
+ run: ../../workflows/kallisto/workflow.cwl
+ in:
+ IndexInput: IndexInput
+ InputReadsMultipleSamples: InputReadsMultipleSamples
+ numUnderscoresFileName: numUnderscoresFileName
+ isSingle: isSingle
+ FragmentLength: FragmentLength
+ StandardDeviation: StandardDeviation
+ BootstrapSamples: BootstrapSamples
+ resultsFolder: resultsFolder
+ out: [finalOut]
+
+outputs:
+ finalOut:
+ type: Directory[]
+ outputSource: kallisto/finalOut
diff --git a/runs/kallisto/workflow.yml b/runs/kallisto/run.yml
similarity index 56%
rename from runs/kallisto/workflow.yml
rename to runs/kallisto/run.yml
index 0f8f15d..1d147f9 100644
--- a/runs/kallisto/workflow.yml
+++ b/runs/kallisto/run.yml
@@ -17,22 +17,22 @@ InputReadsMultipleSamples:
- class: File
path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
format: edam:format_1930 # FASTQ
- -
- - class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
- format: edam:format_1930 # FASTQ
- -
- - class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
- format: edam:format_1930 # FASTQ
- -
- - class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
- format: edam:format_1930 # FASTQ
- -
- - class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
- format: edam:format_1930 # FASTQ
+ # -
+ # - class: File
+ # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
+ # format: edam:format_1930 # FASTQ
+ # -
+ # - class: File
+ # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
+ # format: edam:format_1930 # FASTQ
+ # -
+ # - class: File
+ # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
+ # format: edam:format_1930 # FASTQ
+ # -
+ # - class: File
+ # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
+ # format: edam:format_1930 # FASTQ
numUnderscoresFileName: 2
@@ -42,7 +42,7 @@ FragmentLength: 200
StandardDeviation: 20
BootstrapSamples: 30
-resultsFolder: kallisto_results
+resultsFolder: test
$namespaces:
edam: https://edamontology.org/
\ No newline at end of file
diff --git a/workflows/.gitkeep b/workflows/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/workflows/kallisto/kallisto-index.cwl b/workflows/kallisto/kallisto-index.cwl
index 3d29b9e..d35f520 100644
--- a/workflows/kallisto/kallisto-index.cwl
+++ b/workflows/kallisto/kallisto-index.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
hints:
DockerRequirement:
- dockerPull: quay.io/biocontainers/kallisto:0.50.1--h6de1650_2
+ dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
SoftwareRequirement:
packages:
kallisto:
diff --git a/workflows/kallisto/kallisto-quant.cwl b/workflows/kallisto/kallisto-quant.cwl
index 6d3e357..026f7e1 100755
--- a/workflows/kallisto/kallisto-quant.cwl
+++ b/workflows/kallisto/kallisto-quant.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
hints:
DockerRequirement:
- dockerPull: quay.io/biocontainers/kallisto:0.50.1--h6de1650_2
+ dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
SoftwareRequirement:
packages:
kallisto:
diff --git a/workflows/kallisto/kallisto-workflow.cwl b/workflows/kallisto/workflow.cwl
similarity index 100%
rename from workflows/kallisto/kallisto-workflow.cwl
rename to workflows/kallisto/workflow.cwl
--
GitLab