mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 06:33:09 +00:00
Add motus/merge and biom support
This commit is contained in:
parent
8082c7d108
commit
a0ee82bf43
12 changed files with 241 additions and 13 deletions
|
@ -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: { "${params.outdir}/pipeline_info" },
|
||||
|
|
|
@ -38,4 +38,5 @@ params {
|
|||
run_centrifuge = false
|
||||
run_diamond = false
|
||||
run_motus = true
|
||||
run_profile_standardisation = true
|
||||
}
|
||||
|
|
|
@ -78,8 +78,11 @@
|
|||
"minimap2/index": {
|
||||
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
|
||||
},
|
||||
"motus/merge": {
|
||||
"git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
|
||||
},
|
||||
"motus/profile": {
|
||||
"git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
|
||||
"git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
|
||||
},
|
||||
"multiqc": {
|
||||
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
|
||||
|
|
47
modules/nf-core/modules/motus/merge/main.nf
generated
Normal file
47
modules/nf-core/modules/motus/merge/main.nf
generated
Normal file
|
@ -0,0 +1,47 @@
|
|||
VERSION = '3.0.1'
|
||||
|
||||
process MOTUS_MERGE {
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
|
||||
container "${ 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
57
modules/nf-core/modules/motus/merge/meta.yml
generated
Normal file
|
@ -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
2
modules/nf-core/modules/motus/profile/main.nf
generated
|
@ -48,7 +48,7 @@ process MOTUS_PROFILE {
|
|||
fi
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
mOTUs: \$VERSION
|
||||
motus: \$VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
@ -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
56
subworkflows/local/standardisation_profiles.nf
Normal 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
|
||||
}
|
|
@ -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() )
|
||||
|
|
|
@ -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
|
||||
*/
|
||||
|
|
Loading…
Reference in a new issue