From 78384be5d72fcd06985c29dea3905712db5a2dab Mon Sep 17 00:00:00 2001
From: Sameeul Bashir Samee <sameeul@gmail.com>
Date: Fri, 8 Nov 2024 15:19:16 -0500
Subject: [PATCH] Use ome-converter-tool (#21)

---
 cwl_adapters/ome-converter.cwl | 24 ++----------------------
 workflows/bbbc.py              |  1 -
 workflows/bbbc.wic             |  1 -
 3 files changed, 2 insertions(+), 24 deletions(-)

diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl
index 7dd5607..88d1b83 100644
--- a/cwl_adapters/ome-converter.cwl
+++ b/cwl_adapters/ome-converter.cwl
@@ -10,24 +10,13 @@ doc: |-
 
 requirements:
   DockerRequirement:
-    dockerPull: polusai/ome-converter-plugin:0.3.2-dev2
+    dockerPull: polusai/ome-converter-tool:0.3.3-dev4
   # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement
   InitialWorkDirRequirement:
     listing:
     - entry: $(inputs.outDir)
       writable: true  # Output directories must be writable
   InlineJavascriptRequirement: {}
-# NOTE: polusai/ome-converter-plugin:0.3.1 uses the base image
-# polusai/bfio:2.3.2 which now un-bundles the java maven package
-# ome:formats-gpl:7.1.0 due to licensing reasons.
-# To avoid requiring network access at runtime, in the bfio Dockerfile
-# it is pre-installed and saved in ~/.m2/  However, by default
-# CWL hides all environment variables (including HOME), so we need to
-# set HOME here so that at runtime we get a cache hit on the maven install.
-  EnvVarRequirement:
-# See https://www.commonwl.org/user_guide/topics/environment-variables.html
-    envDef:
-      HOME: /home/polusai
 
 inputs:
   inpDir:
@@ -46,15 +35,6 @@ inputs:
     inputBinding:
       prefix: --filePattern
 
-  fileExtension:
-    label: The file extension
-    doc: |-
-      The file extension
-    type: string
-    inputBinding:
-      prefix: --fileExtension
-    default: "default"  # enum: .ome.tiff, .ome.zarr, default
-
   outDir:
     label: Output collection
     doc: |-
@@ -78,4 +58,4 @@ $namespaces:
 $schemas:
 - https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
 
-# manifest: https://raw.githubusercontent.com/PolusAI/polus-plugins/master/formats/ome-converter-plugin/plugin.json
\ No newline at end of file
+# manifest: https://raw.githubusercontent.com/PolusAI/polus-plugins/master/formats/ome-converter-plugin/plugin.json
diff --git a/workflows/bbbc.py b/workflows/bbbc.py
index 53edb54..de03ccd 100644
--- a/workflows/bbbc.py
+++ b/workflows/bbbc.py
@@ -22,7 +22,6 @@ def workflow() -> Workflow:
     omeconverter = Step(clt_path='../image-workflows/cwl_adapters/ome-converter.cwl')
     omeconverter.inpDir = filerenaming.outDir
     omeconverter.filePattern = '.*.tif'
-    omeconverter.fileExtension = '.ome.tif'
     omeconverter.outDir = Path('omeconverter.outDir')
 
     montage = Step(clt_path='../image-workflows/cwl_adapters/montage.cwl')
diff --git a/workflows/bbbc.wic b/workflows/bbbc.wic
index 7f650d9..67cde4b 100644
--- a/workflows/bbbc.wic
+++ b/workflows/bbbc.wic
@@ -21,7 +21,6 @@ steps:
     - outDir: !& file-renaming.outDir
   ome-converter:
     in:
-      fileExtension: !ii .ome.tif
       filePattern: !ii .*.tif
       inpDir: !* file-renaming.outDir
       outDir: !ii omeconverter.outDir