Fix bug with Fusion symlink resolution (#4593)

This commit is a supplement to PR #4348 to fix the issue #4309 Signed-off-by: Ben Sherman <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]> Co-authored-by: Paolo Di Tommaso <[email protected]>
nextflow-io · Dec 17, 2023 · 9a58236 · 9a58236
1 parent 4bd660b
commit 9a58236
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diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
@@ -134,7 +134,7 @@ class PublishDir {
     }
 
     protected Map<String,Path> getTaskInputs() {
-        return task?.getInputFilesMap()
+        return task ? task.getInputFilesMap() : Map.<String,Path>of()
     }
 
     void setPath( def value ) {
@@ -294,6 +294,7 @@ class PublishDir {
         this.sourceDir = task.targetDir
         this.sourceFileSystem = sourceDir.fileSystem
         this.stageInMode = task.config.stageInMode
+        this.task = task
 
         apply0(files)
     }

diff --git a/tests/checks/fusion-symlink.nf/.checks b/tests/checks/fusion-symlink.nf/.checks
@@ -10,6 +10,7 @@ fi
 # normal run
 #
 echo initial run
+$NXF_CMD fs rm s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt || true
 $NXF_RUN -c .config
 
 $NXF_CMD fs cp s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt data.txt
@@ -19,6 +20,7 @@ cmp data.txt .expected || false
 # resume run
 #
 echo resumed run
+$NXF_CMD fs rm s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt || true
 $NXF_RUN -c .config -resume
 
 $NXF_CMD fs cp s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt data.txt