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Merge pull request #137 from nf-core/motus-merge-meta

Standardise mOTUs table merge
This commit is contained in:
James A. Fellows Yates 2022-09-16 16:01:38 +02:00 committed by GitHub
commit a2a9f458ec
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5 changed files with 22 additions and 12 deletions

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@ -418,6 +418,8 @@ process {
}
withName: MOTUS_MERGE {
ext.args = { params.generate_biom_output ? "-B" : "" }
ext.prefix = { "motus_${meta.id}_combined_reports" }
publishDir = [
path: { "${params.outdir}/motus/" },
mode: params.publish_dir_mode

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@ -111,7 +111,7 @@
},
"motus/merge": {
"branch": "master",
"git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
"git_sha": "54ff289487244bf15543ecfa62bd4df49be72b73"
},
"motus/profile": {
"branch": "master",

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@ -1,6 +1,7 @@
VERSION = '3.0.1'
process MOTUS_MERGE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
@ -9,14 +10,13 @@ process MOTUS_MERGE {
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
input:
path input
tuple val(meta), path(input)
path db // to stop docker saying it can't find it... would have to have the module in upstream steps anyway
path profile_version_yml, stageAs: 'profile_version.yml'
val biom_format
output:
path("*.txt") , optional: true, emit: txt
path("*.biom"), optional: true, emit: biom
tuple val(meta), path("*.txt") , optional: true, emit: txt
tuple val(meta), path("*.biom"), optional: true, emit: biom
path "versions.yml" , emit: versions
when:
@ -24,16 +24,16 @@ process MOTUS_MERGE {
script:
def args = task.ext.args ?: ''
def prefix = 'motus_merged'
def prefix = task.ext.prefix ?: "${meta.id}"
def cmd_input = input.size() > 1 ? "-i ${input.join(',')}" : input.isDirectory() ? "-d ${input}" : "-i ${input}"
def output = biom_format ? "-B -o ${prefix}.biom" : "-o ${prefix}.txt"
def suffix = task.ext.args?.contains("-B") ? "biom" : "txt"
"""
motus \\
merge \\
-db $db \\
${cmd_input} \\
$args \\
${output}
-o ${prefix}.${suffix}
## Take version from the mOTUs/profile module output, as cannot reconstruct
## version without having database staged in this directory.

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@ -35,9 +35,6 @@ input:
this itself without having the motus database present and configured with the tool
so here we take it from what is already reported by the upstream module.
pattern: "versions.yml"
- biom_format:
type: boolean
description: Whether to save output OTU table in biom format
output:
- versions:

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@ -96,10 +96,21 @@ workflow STANDARDISATION_PROFILES {
ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS.out.txt )
ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS.out.versions )
// mOTUs
// mOTUs has a 'single' database, and cannot create custom ones.
// Therefore removing db info here, and publish merged at root mOTUs results
// directory
MOTUS_MERGE ( ch_input_profiles.motus.map{it[1]}.collect(), ch_input_databases.motus.map{it[1]}, motu_version, params.generate_biom_output )
ch_profiles_for_motus = ch_input_profiles.motus
.map { [it[0]['db_name'], it[1]] }
.groupTuple()
.map {
[[id:it[0]], it[1]]
}
MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version )
if ( params.generate_biom_output ) {
ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom )
} else {