port changes

viash-io · Dec 16, 2024 · ffb686e · ffb686e
1 parent 56ed0d2
commit ffb686e
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diff --git a/src/main/resources/io/viash/platforms/nextflow/states/publishStates.nf b/src/main/resources/io/viash/platforms/nextflow/states/publishStates.nf
diff --git a/src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf b/src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf
@@ -42,7 +42,7 @@ process publishFilesProc {
       if (infile.toString() != outfile.toString()) {
         [
           "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "ln '${infile.toString()}' '${outfile.toString()}'"
         ]
       } else {
         // no need to copy if infile is the same as outfile
@@ -73,7 +73,6 @@ def publishFilesByConfig(Map args) {
           def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
           def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
 
-
           // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)