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refactor: make metaphlan3 run in workflow

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This commit is contained in:
Moritz E. Beber 2022-03-18 20:50:18 +01:00
parent 69db920610
commit a425a322f2
3 changed files with 8 additions and 4 deletions
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3
nextflow.config
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@ -71,6 +71,9 @@ params {
// kraken2
run_kraken2 = false
// metaphlan3
run_metaphlan3 = false
}
// Load base.config by default for all pipelines

6
subworkflows/local/input_check.nf
View file

@ -31,9 +31,9 @@ workflow INPUT_CHECK {
.set { fasta }
emit:
fastq // channel: [ val(meta), [ reads ] ]
nanopore // channel: [ val(meta), [ reads ] ]
fasta // channel: [ val(meta), fasta ]
fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ]
nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ]
fasta = fasta ?: [] // channel: [ val(meta), fasta ]
versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
}

3
workflows/taxprofiler.nf
View file

@ -165,9 +165,10 @@ workflow TAXPROFILER {
}
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.dump(tag: "input_metaphlan3")
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
reads: [it[0] + it[2], it[1][0]]
db: it[3]
}