Commit 6fff4400 authored by Thomas Van Parys's avatar Thomas Van Parys
Browse files

Add dummy channels to circumvent join matching bug

parent e32b6c67
......@@ -186,12 +186,20 @@ process download_plaza_fasta{
"""
}
///
//Due to a Nextflow oddity, the .join() operator only works when at least one match is found
//Add a dummy match to both channels, which will be filtered out in the next step.
dummyPlazaChannel = Channel.value(['dummy', 'dummy_cds.fasta', 'dummy_prot.fasta'])
dummyIncompleteChannel = Channel.value([name: 'dummy'])
plaza_fasta.mix(dummyPlazaChannel).set{plaza_fasta}
species_incomplete.mix(dummyIncompleteChannel).set{species_incomplete}
///
species_incomplete
.map { [ it.name , it ] }
.join ( plaza_fasta, remainder: true )
.filter { it[0] != 'dummy' }
.map {
specie = it[1]
if (!specie.cds) specie.cds = it[2]
......
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