mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:03:10 +00:00
Merge branch 'dev' into update_filtlong
This commit is contained in:
commit
3f5fa8cc7a
11 changed files with 196 additions and 5 deletions
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@ -398,6 +398,13 @@ process {
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]
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}
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withName: MOTUS_MERGE {
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publishDir = [
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path: { "${params.outdir}/motus/" },
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mode: params.publish_dir_mode
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]
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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@ -38,4 +38,5 @@ params {
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run_centrifuge = false
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run_diamond = false
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run_motus = true
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run_profile_standardisation = true
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}
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@ -78,6 +78,9 @@
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"minimap2/index": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"motus/merge": {
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"git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
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},
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"motus/profile": {
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"git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
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},
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47
modules/nf-core/modules/motus/merge/main.nf
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47
modules/nf-core/modules/motus/merge/main.nf
generated
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@ -0,0 +1,47 @@
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VERSION = '3.0.1'
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process MOTUS_MERGE {
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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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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
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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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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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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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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 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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"""
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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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## 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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VERSION=\$(cat ${profile_version_yml} | grep '/*motus:.*' | sed 's/.*otus: //g')
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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motus: \$VERSION
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END_VERSIONS
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"""
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}
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57
modules/nf-core/modules/motus/merge/meta.yml
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57
modules/nf-core/modules/motus/merge/meta.yml
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@ -0,0 +1,57 @@
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name: "motus_merge"
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description: Taxonomic meta-omics profiling using universal marker genes
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keywords:
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- classify
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- metagenomics
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- fastq
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- taxonomic profiling
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- merging
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- merge
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- otu table
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tools:
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- "motus":
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description: "Marker gene-based OTU (mOTU) profiling"
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homepage: "https://motu-tool.org/"
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documentation: "https://github.com/motu-tool/mOTUs/wiki"
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tool_dev_url: "https://github.com/motu-tool/mOTUs"
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doi: "10.1038/s41467-019-08844-4"
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licence: "['GPL v3']"
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input:
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- input:
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type: file
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description: |
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List of output files (more than one) from motus profile,
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or a single directory containing motus output files.
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- db:
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type: directory
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description: |
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mOTUs database downloaded by `motus downloadDB`
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pattern: "db_mOTU/"
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- profile_version_yml:
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type: file
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description: |
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A single versions.yml file output from motus/profile. motus/merge cannot reconstruct
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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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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- txt:
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type: file
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description: OTU table in txt format, if BIOM format not requested
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pattern: "*.txt"
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- biom:
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type: file
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description: OTU table in biom format, if BIOM format requested
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pattern: "*.biom"
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authors:
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- "@jfy133"
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@ -132,6 +132,10 @@ params {
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// krona
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run_krona = false
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krona_taxonomy_directory = null
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// profile standardisation
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run_profile_standardisation = false
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generate_biom_output = false
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}
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// Load base.config by default for all pipelines
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@ -52,7 +52,8 @@
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"type": "string",
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"description": "Name of iGenomes reference.",
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"fa_icon": "fas fa-book",
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"help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
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"help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.",
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"hidden": true
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},
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"igenomes_base": {
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"type": "string",
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@ -444,7 +445,13 @@
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},
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"krona_taxonomy_directory": {
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"type": "string",
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"default": null
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"default": "None"
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},
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"run_profile_standardisation": {
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"type": "boolean"
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},
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"generate_biom_output": {
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"type": "boolean"
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}
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}
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}
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@ -228,12 +228,12 @@ workflow PROFILING {
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ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
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ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.map{it[1]} )
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}
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emit:
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classifications = ch_raw_classifications
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profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ] - should be text files or biom
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versions = ch_versions // channel: [ versions.yml ]
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motus_version = params.run_motus ? MOTUS_PROFILE.out.versions.first() : Channel.empty()
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mqc = ch_multiqc_files
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}
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56
subworkflows/local/standardisation_profiles.nf
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56
subworkflows/local/standardisation_profiles.nf
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@ -0,0 +1,56 @@
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//
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// Create Krona visualizations
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//
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include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main'
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workflow STANDARDISATION_PROFILES {
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take:
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classifications
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profiles
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databases
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motu_version
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main:
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ch_standardised_tables = Channel.empty()
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ch_versions = Channel.empty()
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/*
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Split profile results based on tool they come from
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*/
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ch_input_profiles = profiles
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.branch {
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motus: it[0]['tool'] == 'motus'
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unknown: true
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}
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ch_input_classifications = classifications
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.branch {
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unknown: true
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}
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ch_input_databases = databases
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.branch {
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motus: it[0]['tool'] == 'motus'
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unknown: true
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}
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/*
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Standardise and aggregate
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*/
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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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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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ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.txt )
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}
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ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions )
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emit:
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tables = ch_standardised_tables
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versions = ch_versions
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}
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@ -78,7 +78,7 @@ workflow VISUALIZATION_KRONA {
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ch_krona_text_for_import = ch_cleaned_krona_text
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.map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
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.groupTuple()
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.dump(tag: "text")
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KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
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ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
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ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
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@ -92,7 +92,7 @@ workflow VISUALIZATION_KRONA {
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ch_krona_taxonomy_for_input = GUNZIP.out.gunzip
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.map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
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.groupTuple()
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.dump(tag: "taxonomy")
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KRONA_KTIMPORTTAXONOMY ( ch_krona_taxonomy_for_input, file(params.krona_taxonomy_directory, checkExists: true) )
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ch_krona_html.mix( KRONA_KTIMPORTTAXONOMY.out.html )
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ch_versions = ch_versions.mix( MEGAN_RMA2INFO.out.versions.first() )
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@ -65,6 +65,7 @@ include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_h
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include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
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include { PROFILING } from '../subworkflows/local/profiling'
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include { VISUALIZATION_KRONA } from '../subworkflows/local/visualization_krona'
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include { STANDARDISATION_PROFILES } from '../subworkflows/local/standardisation_profiles'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
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}
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/*
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SUBWORKFLOW: PROFILING STANDARDISATION
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*/
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if ( params.run_profile_standardisation ) {
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STANDARDISATION_PROFILES ( PROFILING.out.classifications, PROFILING.out.profiles, DB_CHECK.out.dbs, PROFILING.out.motus_version )
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ch_versions = ch_versions.mix( STANDARDISATION_PROFILES.out.versions )
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}
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/*
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MODULE: MultiQC
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*/
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