From 52c6957830d6c537a6b2308bd364eaac7a6f22c4 Mon Sep 17 00:00:00 2001
From: Jeremy Muhlich <jmuhlich@bitflood.org>
Date: Wed, 16 Oct 2024 17:01:32 -0400
Subject: [PATCH 1/2] Update coreograph to 2.4.0

This version outputs ome-tiff pyramids already so the roadie/pyramidize
step is no longer necessary.
---
 config/defaults.yml |  2 +-
 modules/dearray.nf  | 14 ++++----------
 2 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/config/defaults.yml b/config/defaults.yml
index 70fe72d2..5ba55b87 100644
--- a/config/defaults.yml
+++ b/config/defaults.yml
@@ -33,7 +33,7 @@ modules:
   dearray:
     name: coreograph
     container: labsyspharm/unetcoreograph
-    version: 2.2.9
+    version: 2.4.0
     cmd: python /app/UNetCoreograph.py --outputPath .
     input: --imagePath
   staging:
diff --git a/modules/dearray.nf b/modules/dearray.nf
index d2ec7ede..ff6193cc 100644
--- a/modules/dearray.nf
+++ b/modules/dearray.nf
@@ -1,13 +1,11 @@
 import mcmicro.*
 
-include {roadie} from "$projectDir/roadie"
-
 process coreograph {
     container "${params.contPfx}${module.container}:${module.version}"
     
-    // Output -- publish masks only, images need to be pyramidized
+    // Output
     publishDir "${params.in}/dearray", mode: "${params.publish_dir_mode}",
-      pattern: '**mask.tif'
+      pattern: '{*.ome.tif,**mask.tif}'
 
     // QC
     publishDir "${Flow.QC(params.in, module.name)}",
@@ -24,7 +22,7 @@ process coreograph {
       path s
     
     output:
-      path "**{,[A-Z],[A-Z][A-Z]}{[0-9],[0-9][0-9]}.tif", emit: cores
+      path "*.ome.tif", emit: cores
       path "**_mask.tif", emit: masks
       path "TMA_MAP.tif"
       path "centroidsY-X.txt"
@@ -45,11 +43,7 @@ workflow dearray {
   main:
     coreograph(mcp, mcp.modules['dearray'], tma)
 
-    // Pass the core images through palom to pyramidize them
-    inputs = coreograph.out.cores.flatten()
-    roadie('pyramidize', inputs, '', true, "${params.in}/dearray", "${params.publish_dir_mode}")
-
   emit:
-    cores = roadie.out
+    cores = coreograph.out.cores.flatten()
     masks = coreograph.out.masks.flatten()
 }

From 69887acac52baa31343fb54c467efc302c5bf94e Mon Sep 17 00:00:00 2001
From: Artem Sokolov <artem.sokolov@gmail.com>
Date: Wed, 16 Oct 2024 19:02:12 -0400
Subject: [PATCH 2/2] Version bump for actions/upload-artifact

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6077bb7f..4b5f9000 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -111,7 +111,7 @@ jobs:
           ./nextflow main.nf --in ~/data/exemplar-001 ${{ matrix.params }}
           ls -R ~/data/exemplar-001
       - name: Upload processed result
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         if: ${{ github.event_name == 'push' && contains(matrix.params, 'viz') }}
         with:
           name: exemplar-001