From 67b2c7569b3ce619526bb3df909afc7e6bfc506d Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 25 Mar 2025 10:42:23 +0100
Subject: [PATCH 1/2] add orthofinder

---
 orthofinder/orthofinder.cwl | 60 +++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100755 orthofinder/orthofinder.cwl

diff --git a/orthofinder/orthofinder.cwl b/orthofinder/orthofinder.cwl
new file mode 100755
index 0000000..5bae29d
--- /dev/null
+++ b/orthofinder/orthofinder.cwl
@@ -0,0 +1,60 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: CommandLineTool
+label: "OrthoFinder"
+doc: |
+  
+  OrthoFinder: phylogenetic orthology inference for comparative genomics
+
+  SIMPLE USAGE:
+  Run full OrthoFinder analysis on FASTA format proteomes in <dir>
+  orthofinder [options] -f <dir>
+
+  Source: https://github.com/davidemms/OrthoFinder
+
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing: 
+      - $(inputs.sequences)
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/orthofinder:2.5.5--hdfd78af_2
+  SoftwareRequirement:
+    packages:
+      - package: OrthoFinder
+        version: [ "2.5.5" ]
+        specs: [ https://identifiers.org/rrid/RRID:SCR_017118 ]    
+  ResourceRequirement:
+    ramMin: $(16 * 1024)
+    coresMin: 4
+
+inputs:
+  sequences:
+    type: File[]
+    format: edam:format_1929
+    label: "FASTA sequence files"
+    doc: |
+      "OrthoFinder requires a writeable directory of sequence files as input (`-f <dir>`). 
+      Hence the files are staged via `InitialWorkDirRequirement` and passed as $(runtime.outdir) to argument -f."
+
+outputs:
+  OrthoFinderOutDir:
+    type: Directory
+    doc: "OrthoFinder outputs a directory OrthoFinder/Results_<date in MMMDD format>"
+    outputBinding:
+      glob: OrthoFinder/Results*
+
+baseCommand: orthofinder
+
+arguments:
+  - prefix: -f
+    valueFrom: $(runtime.outdir)
+
+$namespaces:
+  edam: https://edamontology.org/
+  s: https://schema.org/
+$schemas:
+  - https://edamontology.org/EDAM_1.25.owl
+  - https://schema.org/version/latest/schemaorg-current-https.rdf

From 23fa633776b1be869f394d15d218fcb192828a25 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 25 Mar 2025 10:43:07 +0100
Subject: [PATCH 2/2] change CWL version to 1.0

---
 orthofinder/orthofinder.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/orthofinder/orthofinder.cwl b/orthofinder/orthofinder.cwl
index 5bae29d..f02a7c0 100755
--- a/orthofinder/orthofinder.cwl
+++ b/orthofinder/orthofinder.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: v1.2
+cwlVersion: v1.0
 class: CommandLineTool
 label: "OrthoFinder"
 doc: |