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Merge pull request #137 from nf-core/motus-merge-meta
Standardise mOTUs table merge
This commit is contained in:
commit
a2a9f458ec
5 changed files with 22 additions and 12 deletions
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@ -418,6 +418,8 @@ process {
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}
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withName: MOTUS_MERGE {
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ext.args = { params.generate_biom_output ? "-B" : "" }
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ext.prefix = { "motus_${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/motus/" },
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mode: params.publish_dir_mode
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@ -111,7 +111,7 @@
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},
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"motus/merge": {
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"branch": "master",
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"git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
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"git_sha": "54ff289487244bf15543ecfa62bd4df49be72b73"
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},
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"motus/profile": {
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"branch": "master",
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14
modules/nf-core/modules/motus/merge/main.nf
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14
modules/nf-core/modules/motus/merge/main.nf
generated
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@ -1,6 +1,7 @@
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VERSION = '3.0.1'
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process MOTUS_MERGE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
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@ -9,14 +10,13 @@ process MOTUS_MERGE {
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'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
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input:
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path input
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tuple val(meta), path(input)
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path db // to stop docker saying it can't find it... would have to have the module in upstream steps anyway
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path profile_version_yml, stageAs: 'profile_version.yml'
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val biom_format
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output:
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path("*.txt") , optional: true, emit: txt
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path("*.biom"), optional: true, emit: biom
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tuple val(meta), path("*.txt") , optional: true, emit: txt
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tuple val(meta), path("*.biom"), optional: true, emit: biom
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path "versions.yml" , emit: versions
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when:
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@ -24,16 +24,16 @@ process MOTUS_MERGE {
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script:
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def args = task.ext.args ?: ''
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def prefix = 'motus_merged'
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def prefix = task.ext.prefix ?: "${meta.id}"
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def cmd_input = input.size() > 1 ? "-i ${input.join(',')}" : input.isDirectory() ? "-d ${input}" : "-i ${input}"
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def output = biom_format ? "-B -o ${prefix}.biom" : "-o ${prefix}.txt"
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def suffix = task.ext.args?.contains("-B") ? "biom" : "txt"
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"""
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motus \\
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merge \\
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-db $db \\
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${cmd_input} \\
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$args \\
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${output}
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-o ${prefix}.${suffix}
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## Take version from the mOTUs/profile module output, as cannot reconstruct
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## version without having database staged in this directory.
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3
modules/nf-core/modules/motus/merge/meta.yml
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3
modules/nf-core/modules/motus/merge/meta.yml
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@ -35,9 +35,6 @@ input:
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this itself without having the motus database present and configured with the tool
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so here we take it from what is already reported by the upstream module.
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pattern: "versions.yml"
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- biom_format:
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type: boolean
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description: Whether to save output OTU table in biom format
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output:
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- versions:
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@ -96,10 +96,21 @@ workflow STANDARDISATION_PROFILES {
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ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS.out.txt )
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ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS.out.versions )
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// mOTUs
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// mOTUs has a 'single' database, and cannot create custom ones.
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// Therefore removing db info here, and publish merged at root mOTUs results
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// directory
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MOTUS_MERGE ( ch_input_profiles.motus.map{it[1]}.collect(), ch_input_databases.motus.map{it[1]}, motu_version, params.generate_biom_output )
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ch_profiles_for_motus = ch_input_profiles.motus
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.map { [it[0]['db_name'], it[1]] }
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.groupTuple()
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.map {
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[[id:it[0]], it[1]]
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}
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MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version )
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if ( params.generate_biom_output ) {
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ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom )
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} else {
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