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Handle case where fastq_dir is a symlink #128

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Merged
fasterius merged 1 commit into from
Nov 24, 2025
Merged

Handle case where fastq_dir is a symlink #128

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7 changes: 7 additions & 0 deletions subworkflows/local/input_check/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,13 @@ def create_channel_spaceranger(meta, fastq_dir) {
meta["id"] = meta.get("sample")
def slide = meta.get("slide")
def area = meta.get("area")

// Resolve symlinks for local filesystem paths only
def scheme = fastq_dir.toUri().getScheme()
if (scheme == null || scheme == 'file') {
fastq_dir = fastq_dir.toRealPath() // resolve symlink (if applicable)
}

def fastq_files = fastq_dir.listFiles().findAll { file ->
file.name.endsWith('.fastq.gz')
}
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