millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-25 09:29:55 +00:00
Code Issues Releases Packages Activity

Typos

Browse source
This commit is contained in:
James Fellows Yates 2022-04-18 07:28:09 +02:00
parent 564474cafe
commit 6307a9cf43
2 changed files with 2 additions and 2 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
subworkflows/local/profiling.nf
View file

@ -76,7 +76,7 @@ workflow PROFILING {
ch_input_for_centrifuge = ch_input_for_profiling.centrifuge ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
.filter{ .filter{
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id
!it[0].is_fasta !it[0].is_fasta
} }
.multiMap { .multiMap {

2
workflows/taxprofiler.nf
View file

@ -19,7 +19,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
// Check mandatory parameters // Check mandatory parameters
if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' } if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler]: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files." if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs" if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." } if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }