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Make sure fasta and spectral_library are always a Channel
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When these files are stored locally they are initialized as a file
system object, but when they are downloaded from panorama they are a
channel. This inconsistency was causing problems with the
combine_file_hashes sub-workflow.
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ajmaurais committed Sep 18, 2024
1 parent 6274fc2 commit 3c7cd87
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions workflows/get_input_files.nf
Original file line number Diff line number Diff line change
Expand Up @@ -46,15 +46,15 @@ workflow get_input_files {
PANORAMA_GET_FASTA(params.fasta, aws_secret_id)
fasta = PANORAMA_GET_FASTA.out.panorama_file
} else {
fasta = file(params.fasta, checkIfExists: true)
fasta = Channel.value(file(params.fasta, checkIfExists: true))
}

if(params.spectral_library) {
if(params.spectral_library.startsWith(PANORAMA_URL)) {
PANORAMA_GET_SPECTRAL_LIBRARY(params.spectral_library, aws_secret_id)
spectral_library = PANORAMA_GET_SPECTRAL_LIBRARY.out.panorama_file
} else {
spectral_library = file(params.spectral_library, checkIfExists: true)
spectral_library = Channel.value(file(params.spectral_library, checkIfExists: true))
}
} else {
spectral_library = null
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