From 225773000f82f23053b72ca523c9b7aeecf261e8 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 31 Jan 2023 12:00:48 +0100 Subject: [PATCH] Fix channel structure when supplying own host bt2 index --- workflows/taxprofiler.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index 7a09573..12a41f3 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -38,7 +38,7 @@ if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { exi if (!params.hostremoval_reference && params.hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." } if (params.hostremoval_reference ) { ch_reference = file(params.hostremoval_reference) } -if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = file(params.shortread_hostremoval_index ) } else { ch_shortread_reference_index = [] } +if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = Channel.fromPath(params.shortread_hostremoval_index).map{[[], it]} } else { ch_shortread_reference_index = [] } if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] } if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. As --diamond_save_reads supplied, only aligned reads in SAM format will be produced, no taxonomic profiles will be available."