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Ensure merge metaphlan3 tables happens on per database basis
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parent
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commit
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7 changed files with 22 additions and 12 deletions
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@ -96,11 +96,11 @@
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},
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"metaphlan3/mergemetaphlantables": {
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"branch": "master",
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"git_sha": "940d7fe9d63962e0e2ba0987e2893fb0aff832e3"
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"git_sha": "36bcd675ae76a379a38165898a203f4915823f4f"
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},
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"metaphlan3/metaphlan3": {
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"branch": "master",
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"git_sha": "940d7fe9d63962e0e2ba0987e2893fb0aff832e3"
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"git_sha": "978087354eb72ac1f6e18a3f790fad9bc4d05840"
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},
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"minimap2/align": {
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"branch": "master",
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@ -7,10 +7,10 @@ process METAPHLAN3_MERGEMETAPHLANTABLES {
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'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
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input:
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path(profiles)
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tuple val(meta), path(profiles)
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output:
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tuple path("${prefix}.txt") , emit: txt
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tuple val(meta), path("${prefix}.txt") , emit: txt
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path "versions.yml" , emit: versions
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when:
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@ -18,7 +18,7 @@ process METAPHLAN3_MERGEMETAPHLANTABLES {
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "merged_abundance_table"
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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merge_metaphlan_tables.py \\
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$args \\
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@ -15,12 +15,22 @@ tools:
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licence: ["MIT License"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- profiles:
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type: file
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description: List of per-sample MetaPhlAn3 taxonomic abundance tables
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pattern: "*"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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@ -1,4 +1,4 @@
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process METAPHLAN3 {
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process METAPHLAN3_METAPHLAN3 {
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tag "$meta.id"
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label 'process_high'
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@ -1,4 +1,4 @@
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name: metaphlan3
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name: metaphlan3_metaphlan3
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description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
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keywords:
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- metagenomics
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@ -7,7 +7,7 @@ include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/mo
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include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main'
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include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
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include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main'
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include { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/metaphlan3/main'
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include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/metaphlan3/main'
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include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main'
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include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main'
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include { MOTUS_PROFILE } from '../../modules/nf-core/modules/motus/profile/main'
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@ -168,9 +168,9 @@ workflow PROFILING {
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db: it[3]
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}
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METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
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ch_versions = ch_versions.mix( METAPHLAN3.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( METAPHLAN3.out.biom )
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METAPHLAN3_METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
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ch_versions = ch_versions.mix( METAPHLAN3_METAPHLAN3.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( METAPHLAN3_METAPHLAN3.out.profile )
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}
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@ -65,7 +65,7 @@ workflow STANDARDISATION_PROFILES {
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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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[it[1]]
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[[id:it[0]], it[1]]
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}
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METAPHLAN3_MERGEMETAPHLANTABLES ( ch_profiles_for_metaphlan3 )
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