millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-22 09:39:54 +00:00
Code Issues Releases Packages Activity

Fix channel structure when supplying own host bt2 index

Browse source
This commit is contained in:
James Fellows Yates 2023-01-31 12:00:48 +01:00
parent 43a503096e
commit 225773000f
1 changed files with 1 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
workflows/taxprofiler.nf
View file

@ -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 && 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.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.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." 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."