From cb06bbb8b5c525777e1949f1f878d0821e1caf96 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 2 Aug 2024 16:48:29 +0200
Subject: [PATCH] trying to fix use of R with CWL
---
renv.Rmd | 0
runs/kallisto/README.md | 2 +-
runs/kallisto_collect/README.md | 6 ++++++
runs/kallisto_collect/run.yml | 8 ++------
workflows/kallisto_collect/kallisto_collect.R | 11 ++++++++---
.../kallisto_collect/kallisto_collect.cwl | 19 ++++++++++++-------
.../kallisto_sleuth/kallisto_sleuth.cwl | 0
7 files changed, 29 insertions(+), 17 deletions(-)
create mode 100644 renv.Rmd
create mode 100644 runs/kallisto_collect/README.md
rename runs/kallisto_collect/run.cwl => workflows/kallisto_collect/kallisto_collect.cwl (69%)
rename runs/kallisto_sleuth/run.cwl => workflows/kallisto_sleuth/kallisto_sleuth.cwl (100%)
diff --git a/renv.Rmd b/renv.Rmd
new file mode 100644
index 0000000..e69de29
diff --git a/runs/kallisto/README.md b/runs/kallisto/README.md
index 2f01d07..e3c73f3 100644
--- a/runs/kallisto/README.md
+++ b/runs/kallisto/README.md
@@ -1,6 +1,6 @@
# Kallisto Workflow
-## Executing individual steps
+## Executing the multi-step workflow
```bash
cd runs/kallisto/
diff --git a/runs/kallisto_collect/README.md b/runs/kallisto_collect/README.md
new file mode 100644
index 0000000..a680462
--- /dev/null
+++ b/runs/kallisto_collect/README.md
@@ -0,0 +1,6 @@
+
+
+```bash
+cd runs/kallisto_collect/
+cwltool ../../workflows/kallisto_collect/kallisto_collect.cwl run.yml > $(date +"%Y-%m-%d_%H-%M").log 2>&1 &
+```
diff --git a/runs/kallisto_collect/run.yml b/runs/kallisto_collect/run.yml
index 2a4197c..ba0dd18 100644
--- a/runs/kallisto_collect/run.yml
+++ b/runs/kallisto_collect/run.yml
@@ -1,10 +1,6 @@
-cores: 1
-r_script:
- class: File
- path: ../../workflows/kallisto_collect/kallisto_collect.R
-in_kallisto_results:
+in_kallisto_results:
class: Directory
- path: ../kallisto_sleuth/out
+ path: ../runs/kallisto/kallisto_results
in_metadata_file:
class: File
path: ../merged_isa_metadata/out/merged_isa.tsv
diff --git a/workflows/kallisto_collect/kallisto_collect.R b/workflows/kallisto_collect/kallisto_collect.R
index 6a24e7e..b2023ff 100644
--- a/workflows/kallisto_collect/kallisto_collect.R
+++ b/workflows/kallisto_collect/kallisto_collect.R
@@ -4,9 +4,14 @@
#### Load required library
################################################
-library(sleuth)
-library(tidyverse)
-library(jsonlite)
+if(!"BiocManager" %in% row.names(installed.packages())){install.packages('BiocManager')}
+
+if(!"sleuth" %in% row.names(installed.packages())){
+ BiocManager::install('pachterlab/sleuth')
+}
+if(!"tidyverse" %in% row.names(installed.packages())){install.packages("tidyverse")}
+if(!"openxlsx" %in% row.names(installed.packages())){install.packages("openxlsx")}
+if(!"jsonlite" %in% row.names(installed.packages())){install.packages("jsonlite")}
################################################
#### Read arguments from CLI
diff --git a/runs/kallisto_collect/run.cwl b/workflows/kallisto_collect/kallisto_collect.cwl
similarity index 69%
rename from runs/kallisto_collect/run.cwl
rename to workflows/kallisto_collect/kallisto_collect.cwl
index eaee053..6428310 100644
--- a/runs/kallisto_collect/run.cwl
+++ b/workflows/kallisto_collect/kallisto_collect.cwl
@@ -3,11 +3,19 @@
cwlVersion: v1.2
class: CommandLineTool
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: kallisto_collect.R
+ entry:
+ $include: kallisto_collect.R
+ - class: NetworkAccess
+ networkAccess: true
+
+baseCommand: [Rscript, kallisto_collect.R]
+
inputs:
-- id: r_script
- type: File
- inputBinding:
- position: 0
+
- id: in_kallisto_results
type: Directory
inputBinding:
@@ -36,6 +44,3 @@ outputs:
items: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
diff --git a/runs/kallisto_sleuth/run.cwl b/workflows/kallisto_sleuth/kallisto_sleuth.cwl
similarity index 100%
rename from runs/kallisto_sleuth/run.cwl
rename to workflows/kallisto_sleuth/kallisto_sleuth.cwl
--
GitLab