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refactor: make metaphlan3 run in workflow
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3 changed files with 8 additions and 4 deletions
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@ -71,6 +71,9 @@ params {
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// kraken2
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run_kraken2 = false
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// metaphlan3
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run_metaphlan3 = false
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}
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// Load base.config by default for all pipelines
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@ -31,9 +31,9 @@ workflow INPUT_CHECK {
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.set { fasta }
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emit:
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fastq // channel: [ val(meta), [ reads ] ]
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nanopore // channel: [ val(meta), [ reads ] ]
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fasta // channel: [ val(meta), fasta ]
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fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ]
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nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ]
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fasta = fasta ?: [] // channel: [ val(meta), fasta ]
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versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
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}
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@ -165,9 +165,10 @@ workflow TAXPROFILER {
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}
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ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
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.dump(tag: "input_metaphlan3")
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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reads: [it[0] + it[2], it[1][0]]
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db: it[3]
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}
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