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Debug: try ln instead of cp -r #779

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Debug: try ln instead of cp -r #779

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0c2f29e
try whether ln instead of cp -r works
rcannood Dec 4, 2024
56ed0d2
Merge remote-tracking branch 'origin/develop' into ln-instead-cp-r
rcannood Dec 16, 2024
ffb686e
port changes
rcannood Dec 16, 2024
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3 changes: 1 addition & 2 deletions src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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)
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