millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-22 08:29:54 +00:00
Code Issues Releases Packages Activity

Tweak DIAMOND save_reads message

Browse source
This commit is contained in:
James Fellows Yates 2022-06-03 13:55:17 +02:00
parent 3313b90453
commit d48b3be5a7
2 changed files with 2 additions and 2 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
nextflow.config
View file

@ -124,7 +124,7 @@ params {
// diamond // diamond
run_diamond = false run_diamond = false
diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently
diamond_save_reads = false // this will override diamound output format so no taxonomic profile is generated! diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated!
} }
// Load base.config by default for all pipelines // Load base.config by default for all pipelines

2
workflows/taxprofiler.nf
View file

@ -33,7 +33,7 @@ if (params.hostremoval_reference ) { ch_reference = file(params.hostre
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 = file(params.shortread_hostremoval_index ) } 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. 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."
/* /*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~