From cf6b077958898be37720a1d0a162c674d60296b3 Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Sat, 7 Sep 2024 17:21:26 -0700
Subject: [PATCH] fix Windows paths

---
 .../nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy    | 4 ----
 .../src/test/nextflow/quilt/QuiltObserverTest.groovy         | 5 +++--
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy
index 1f1f5e39..14904e40 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy
@@ -116,15 +116,11 @@ class QuiltObserver implements TraceObserver {
 
     String workRelative(Path src) {
         Path source = src.toAbsolutePath().normalize()
-        log.debug("workRelative.source: $source [type: ${source.getClass()}]")
         Path workDir = session.workDir.toAbsolutePath().normalize()
-        log.debug("workRelative.workDir: $workDir [type: ${workDir.getClass()}]")
         try {
             Path subPath = workDir.relativize(source)
-            log.debug("workRelative.subPath: $subPath]")
             // drop first two components, which are the workDir
             Path relPath = subPath.subpath(2, subPath.getNameCount())
-            log.debug("workRelative.relPath: $relPath]")
             return relPath.toString()
         } catch (IllegalArgumentException e) {
             log.error("workRelative.fallback: $e")
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy
index 6b838733..bda8b037 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy
+++ b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy
@@ -18,6 +18,7 @@ package nextflow.quilt.nio
 
 import nextflow.quilt.QuiltSpecification
 import nextflow.quilt.QuiltObserver
+import nextflow.quilt.jep.QuiltPackage
 import nextflow.Session
 
 import java.nio.file.Path
@@ -90,7 +91,7 @@ class QuiltObserverTest extends QuiltSpecification {
         expect:
         String relPath = observer.workRelative(source)
         println("relPath: $relPath")
-        relPath == subPath
+        relPath == QuiltPackage.osConvert(subPath)
         println('done')
     }
 
@@ -136,7 +137,7 @@ class QuiltObserverTest extends QuiltSpecification {
         given:
         QuiltObserver observer = makeObserver()
         expect:
-        observer.session.workDir.toString() == './work'
+        observer.session.workDir.toString() == QuiltPackage.osConvert('./work')
         rc == observer.canOverlayPath(Paths.get(path), Paths.get(path))
         where:
         rc    | path