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Use id column from samplesheet if specified #8

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Aug 17, 2023
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Use id column from samplesheet if specified #8

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7 changes: 6 additions & 1 deletion subworkflows/samplesheet_split.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,12 @@ workflow SAMPLESHEET_SPLIT {
.map {
row ->
def meta = [:]
meta.id = file(row.image).simpleName
if (row.id ) {
meta.id = row.id
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Is this id a synapse id?

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@adamjtaylor adamjtaylor Aug 17, 2023 •
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For HTAN we would use a Synapse ID, but this could be used any time you don't want the output directories to be named by the filename and want to provide a custom ID in their place

} else {
meta.id = file(row.image).simpleName

}
meta.ome = row.image ==~ /.+\.ome\.tif{1,2}$/
meta.convert = row.convert.toBoolean()
meta.he = row.he.toBoolean()
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