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Add motus/merge and biom support

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This commit is contained in:
James Fellows Yates 2022-07-12 11:39:26 +02:00
parent 8082c7d108
commit a0ee82bf43
12 changed files with 241 additions and 13 deletions
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8
conf/modules.config
View file

@ -391,12 +391,20 @@ process {
}
withName: MOTUS_PROFILE {
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/motus/${meta.db_name}" },
mode: params.publish_dir_mode
]
}
withName: MOTUS_MERGE {
publishDir = [
path: { "${params.outdir}/motus/" },
mode: params.publish_dir_mode
]
}
withName: CUSTOM_DUMPSOFTWAREVERSIONS {
publishDir = [
path: { "${params.outdir}/pipeline_info" },

1
conf/test_motus.config
View file

@ -38,4 +38,5 @@ params {
run_centrifuge = false
run_diamond = false
run_motus = true
run_profile_standardisation = true
}

5
modules.json
View file

@ -78,8 +78,11 @@
"minimap2/index": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"motus/merge": {
"git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
},
"motus/profile": {
"git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
"git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
},
"multiqc": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

47
modules/nf-core/modules/motus/merge/main.nf generated Normal file
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@ -0,0 +1,47 @@
VERSION = '3.0.1'
process MOTUS_MERGE {
label 'process_low'
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
input:
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
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = 'motus_merged'
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"
"""
motus \\
merge \\
-db $db \\
${cmd_input} \\
$args \\
${output}
## Take version from the mOTUs/profile module output, as cannot reconstruct
## version without having database staged in this directory.
VERSION=\$(cat ${profile_version_yml} | grep '/*motus:.*' | sed 's/.*otus: //g')
cat <<-END_VERSIONS > versions.yml
"${task.process}":
motus: \$VERSION
END_VERSIONS
"""
}

57
modules/nf-core/modules/motus/merge/meta.yml generated Normal file
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@ -0,0 +1,57 @@
name: "motus_merge"
description: Taxonomic meta-omics profiling using universal marker genes
keywords:
- classify
- metagenomics
- fastq
- taxonomic profiling
- merging
- merge
- otu table
tools:
- "motus":
description: "Marker gene-based OTU (mOTU) profiling"
homepage: "https://motu-tool.org/"
documentation: "https://github.com/motu-tool/mOTUs/wiki"
tool_dev_url: "https://github.com/motu-tool/mOTUs"
doi: "10.1038/s41467-019-08844-4"
licence: "['GPL v3']"
input:
- input:
type: file
description: |
List of output files (more than one) from motus profile,
or a single directory containing motus output files.
- db:
type: directory
description: |
mOTUs database downloaded by `motus downloadDB`
pattern: "db_mOTU/"
- profile_version_yml:
type: file
description: |
A single versions.yml file output from motus/profile. motus/merge cannot reconstruct
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:
type: file
description: File containing software versions
pattern: "versions.yml"
- txt:
type: file
description: OTU table in txt format, if BIOM format not requested
pattern: "*.txt"
- biom:
type: file
description: OTU table in biom format, if BIOM format requested
pattern: "*.biom"
authors:
- "@jfy133"

2
modules/nf-core/modules/motus/profile/main.nf generated
View file

@ -48,7 +48,7 @@ process MOTUS_PROFILE {
fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mOTUs: \$VERSION
motus: \$VERSION
END_VERSIONS
"""
}

4
nextflow.config
View file

@ -132,6 +132,10 @@ params {
// krona
run_krona = false
krona_taxonomy_directory = null
// profile standardisation
run_profile_standardisation = false
generate_biom_output = false
}
// Load base.config by default for all pipelines

60
nextflow_schema.json
View file

@ -10,7 +10,10 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"required": [
"input",
"outdir"
],
"properties": {
"input": {
"type": "string",
@ -52,7 +55,8 @@
"type": "string",
"description": "Name of iGenomes reference.",
"fa_icon": "fas fa-book",
"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."
"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.",
"hidden": true
},
"igenomes_base": {
"type": "string",
@ -173,7 +177,14 @@
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true
},
"email_on_fail": {
@ -287,7 +298,10 @@
"shortread_qc_tool": {
"type": "string",
"default": "fastp",
"enum": ["fastp", "adapterremoval"]
"enum": [
"fastp",
"adapterremoval"
]
},
"shortread_qc_skipadaptertrim": {
"type": "boolean"
@ -313,7 +327,11 @@
"shortread_complexityfilter_tool": {
"type": "string",
"default": "bbduk",
"enum": ["bbduk", "prinseqplusplus", "fastp"]
"enum": [
"bbduk",
"prinseqplusplus",
"fastp"
]
},
"shortread_complexityfilter_bbduk_windowsize": {
"type": "integer",
@ -329,7 +347,10 @@
"shortread_complexityfilter_prinseqplusplus_mode": {
"type": "string",
"default": "entropy",
"enum": ["entropy", "dust"]
"enum": [
"entropy",
"dust"
]
},
"shortread_complexityfilter_prinseqplusplus_dustscore": {
"type": "number",
@ -385,7 +406,14 @@
"kaiju_taxon_name": {
"type": "string",
"default": "species",
"enum": ["phylum", "class", "order", "family", "genus", "species"]
"enum": [
"phylum",
"class",
"order",
"family",
"genus",
"species"
]
},
"run_diamond": {
"type": "boolean"
@ -393,7 +421,15 @@
"diamond_output_format": {
"type": "string",
"default": "tsv",
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
"enum": [
"blast",
"xml",
"txt",
"daa",
"sam",
"tsv",
"paf"
]
},
"longread_hostremoval_index": {
"type": "string",
@ -444,7 +480,13 @@
},
"krona_taxonomy_directory": {
"type": "string",
"default": null
"default": "None"
},
"run_profile_standardisation": {
"type": "boolean"
},
"generate_biom_output": {
"type": "boolean"
}
}
}

1
subworkflows/local/profiling.nf
View file

@ -234,5 +234,6 @@ workflow PROFILING {
classifications = ch_raw_classifications
profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ] - should be text files or biom
versions = ch_versions // channel: [ versions.yml ]
motu_version = MOTUS_PROFILE.out.versions.first()
mqc = ch_multiqc_files
}

56
subworkflows/local/standardisation_profiles.nf Normal file
View file

@ -0,0 +1,56 @@
//
// Create Krona visualizations
//
include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main'
workflow STANDARDISATION_PROFILES {
take:
classifications
profiles
databases
motu_version
main:
ch_standardised_tables = Channel.empty()
ch_versions = Channel.empty()
/*
Split profile results based on tool they come from
*/
ch_input_profiles = profiles
.branch {
motus: it[0]['tool'] == 'motus'
unknown: true
}
ch_input_classifications = classifications
.branch {
unknown: true
}
ch_input_databases = databases
.branch {
motus: it[0]['tool'] == 'motus'
unknown: true
}
/*
Standardise and aggregate
*/
// 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 )
if ( params.generate_biom_output ) {
ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom )
} else {
ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.txt )
}
ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions )
emit:
tables = ch_standardised_tables
versions = ch_versions
}

4
subworkflows/local/visualization_krona.nf
View file

@ -78,7 +78,7 @@ workflow VISUALIZATION_KRONA {
ch_krona_text_for_import = ch_cleaned_krona_text
.map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
.groupTuple()
.dump(tag: "text")
KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
@ -92,7 +92,7 @@ workflow VISUALIZATION_KRONA {
ch_krona_taxonomy_for_input = GUNZIP.out.gunzip
.map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
.groupTuple()
.dump(tag: "taxonomy")
KRONA_KTIMPORTTAXONOMY ( ch_krona_taxonomy_for_input, file(params.krona_taxonomy_directory, checkExists: true) )
ch_krona_html.mix( KRONA_KTIMPORTTAXONOMY.out.html )
ch_versions = ch_versions.mix( MEGAN_RMA2INFO.out.versions.first() )

9
workflows/taxprofiler.nf
View file

@ -65,6 +65,7 @@ include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_h
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
include { PROFILING } from '../subworkflows/local/profiling'
include { VISUALIZATION_KRONA } from '../subworkflows/local/visualization_krona'
include { STANDARDISATION_PROFILES } from '../subworkflows/local/standardisation_profiles'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@ -220,6 +221,14 @@ workflow TAXPROFILER {
ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
}
/*
SUBWORKFLOW: PROFILING STANDARDISATION
*/
if ( params.run_profile_standardisation ) {
STANDARDISATION_PROFILES ( PROFILING.out.classifications, PROFILING.out.profiles, DB_CHECK.out.dbs, PROFILING.out.motu_version )
ch_versions = ch_versions.mix( STANDARDISATION_PROFILES.out.versions )
}
/*
MODULE: MultiQC
*/