I have a simple process that stages a remote reference genome:
process StageGenomeReference {
publishDir "resources",
saveAs: it,
mode: "link"
input:
tuple path(uri)
output:
tuple path(uri)
shell:
":"
}
workflow {
channel.of(["https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz"])
}
I believe that in the past, it was staging the file as a hard link, which is what the other processes in my pipeline do when mode: “link” is specified. However, the file here is being published with a symlink instead. I’m wondering if that might have something to do with the file being staged from a remote location, since this is the only process in the pipeline that has this issue and the only one that has this issue?