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Typos
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parent
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2 changed files with 2 additions and 2 deletions
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@ -76,7 +76,7 @@ workflow PROFILING {
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ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
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ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
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.filter{
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.filter{
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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
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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
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!it[0].is_fasta
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!it[0].is_fasta
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}
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}
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.multiMap {
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.multiMap {
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@ -19,7 +19,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
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// Check mandatory parameters
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// Check mandatory parameters
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if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
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if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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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."
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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."
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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"
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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"
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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." }
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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." }
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