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Merge pull request #31 from genomic-medicine-sweden/classification_centrifuge

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Add centrifuge classification (centrifuge/centrifuge module)
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Sofia Stamouli 2022-04-08 11:26:57 +02:00 committed by GitHub
commit 5f24f94391
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12 changed files with 307 additions and 5 deletions
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10
conf/modules.config
View file

@ -198,4 +198,14 @@ process {
]
}
withName: CENTRIFUGE_CENTRIFUGE {
publishDir = [
path: { "${params.outdir}/centrifuge/${meta.db_name}" },
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,txt}'
]
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
}
}

1
conf/test.config
View file

@ -27,6 +27,7 @@ params {
run_kraken2 = true
run_malt = true
run_metaphlan3 = true
run_centrifuge = true
shortread_clipmerge = true
longread_clip = false
shortread_complexityfilter = true

3
modules.json
View file

@ -12,6 +12,9 @@
"cat/fastq": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"centrifuge/centrifuge": {
"git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
},
"custom/dumpsoftwareversions": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},

61
modules/nf-core/modules/centrifuge/centrifuge/main.nf generated Normal file
View file

@ -0,0 +1,61 @@
process CENTRIFUGE_CENTRIFUGE {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
input:
tuple val(meta), path(reads)
path db
val save_unaligned
val save_aligned
val sam_format
output:
tuple val(meta), path('*report.txt') , emit: report
tuple val(meta), path('*results.txt') , emit: results
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
def unaligned = ''
def aligned = ''
if (meta.single_end) {
unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
} else {
unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
}
def sam_output = sam_format ? "--out-fmt 'sam'" : ''
"""
## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
centrifuge \\
-x \$db_name \\
-p $task.cpus \\
$paired \\
--report-file ${prefix}.report.txt \\
-S ${prefix}.results.txt \\
$unaligned \\
$aligned \\
$sam_output \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
END_VERSIONS
"""
}

66
modules/nf-core/modules/centrifuge/centrifuge/meta.yml generated Normal file
View file

@ -0,0 +1,66 @@
name: centrifuge_centrifuge
description: Classifies metagenomic sequence data
keywords:
- classify
- metagenomics
- fastq
- db
tools:
- centrifuge:
description: Centrifuge is a classifier for metagenomic sequences.
homepage: https://ccb.jhu.edu/software/centrifuge/
documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
doi: 10.1101/gr.210641.116
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- db:
type: directory
description: Path to directory containing centrifuge database files
- save_unaligned:
type: value
description: If true unmapped fastq files are saved
- save_aligned:
type: value
description: If true mapped fastq files are saved
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- report:
type: file
description: |
File containing a classification summary
pattern: "*.{report.txt}"
- results:
type: file
description: |
File containing classification results
pattern: "*.{results.txt}"
- fastq_unmapped:
type: file
description: Unmapped fastq files
pattern: "*.unmapped.fastq.gz"
- fastq_mapped:
type: file
description: Mapped fastq files
pattern: "*.mapped.fastq.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@sofstam"
- "@jfy133"
- "@sateeshperi"

5
nextflow.config
View file

@ -84,6 +84,11 @@ params {
// kraken2
run_kraken2 = false
// centrifuge
run_centrifuge = false
centrifuge_save_unaligned = false
centrifuge_save_aligned = false
centrifuge_sam_format = false
// metaphlan3
run_metaphlan3 = false
}

12
nextflow_schema.json
View file

@ -281,6 +281,18 @@
"run_kraken2": {
"type": "boolean"
},
"run_centrifuge": {
"type": "boolean"
},
"centrifuge_save_unaligned": {
"type": "boolean"
},
"centrifuge_save_aligned": {
"type": "boolean"
},
"centrifuge_sam_format": {
"type": "boolean"
},
"run_metaphlan3": {
"type": "boolean",
"description": "Enable MetaPhlAn for taxonomic profiling"

61
nf-core/modules/centrifuge/centrifuge/main.nf Normal file
View file

@ -0,0 +1,61 @@
process CENTRIFUGE_CENTRIFUGE {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
input:
tuple val(meta), path(reads)
path db
val save_unaligned
val save_aligned
val sam_format
output:
tuple val(meta), path('*report.txt') , emit: report
tuple val(meta), path('*results.txt') , emit: results
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
def unaligned = ''
def aligned = ''
if (meta.single_end) {
unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
} else {
unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
}
def sam_output = sam_format ? "--out-fmt 'sam'" : ''
"""
## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
centrifuge \\
-x \$db_name \\
-p $task.cpus \\
$paired \\
--report-file ${prefix}.report.txt \\
-S ${prefix}.results.txt \\
$unaligned \\
$aligned \\
$sam_output \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
END_VERSIONS
"""
}

66
nf-core/modules/centrifuge/centrifuge/meta.yml Normal file
View file

@ -0,0 +1,66 @@
name: centrifuge_centrifuge
description: Classifies metagenomic sequence data
keywords:
- classify
- metagenomics
- fastq
- db
tools:
- centrifuge:
description: Centrifuge is a classifier for metagenomic sequences.
homepage: https://ccb.jhu.edu/software/centrifuge/
documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
doi: 10.1101/gr.210641.116
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- db:
type: directory
description: Path to directory containing centrifuge database files
- save_unaligned:
type: value
description: If true unmapped fastq files are saved
- save_aligned:
type: value
description: If true mapped fastq files are saved
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- report:
type: file
description: |
File containing a classification summary
pattern: "*.{report.txt}"
- results:
type: file
description: |
File containing classification results
pattern: "*.{results.txt}"
- fastq_unmapped:
type: file
description: Unmapped fastq files
pattern: "*.unmapped.fastq.gz"
- fastq_mapped:
type: file
description: Mapped fastq files
pattern: "*.mapped.fastq.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@sofstam"
- "@jfy133"
- "@sateeshperi"

2
subworkflows/local/db_check.nf
View file

@ -22,7 +22,7 @@ workflow DB_CHECK {
ch_dbs_for_untar = parsed_samplesheet
.branch {
untar: it[1].toString().endsWith(".tar.gz") && it[0]['tool'] != 'centrifuge'
untar: it[1].toString().endsWith(".tar.gz")
skip: true
}

7
subworkflows/local/input_check.nf
View file

@ -63,13 +63,12 @@ def create_fastq_channel(LinkedHashMap row) {
if (!file(row.fastq_2).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
}
fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
}
}
return fastq_meta
}
// Function to get list of [ meta, fasta ]
}// Function to get list of [ meta, fasta ]
def create_fasta_channel(LinkedHashMap row) {
def meta = [:]
meta.id = row.sample

18
workflows/taxprofiler.nf
View file

@ -61,6 +61,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/
include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main'
include { MALT_RUN } from '../modules/nf-core/modules/malt/run/main'
include { KRAKEN2_KRAKEN2 } from '../modules/nf-core/modules/kraken2/kraken2/main'
include { CENTRIFUGE_CENTRIFUGE } from '../modules/nf-core/modules/centrifuge/centrifuge/main'
include { METAPHLAN3 } from '../modules/nf-core/modules/metaphlan3/main'
/*
@ -137,6 +138,7 @@ workflow TAXPROFILER {
malt: it[2]['tool'] == 'malt'
kraken2: it[2]['tool'] == 'kraken2'
metaphlan3: it[2]['tool'] == 'metaphlan3'
centrifuge: it[2]['tool'] == 'centrifuge'
unknown: true
}
@ -170,6 +172,18 @@ workflow TAXPROFILER {
db: it[3]
}
// We can run centrifuge one-by-one sample-wise
ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
.dump(tag: "input for centrifuge")
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}
//
// RUN PROFILING
//
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.multiMap {
it ->
@ -188,6 +202,10 @@ workflow TAXPROFILER {
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
}
if ( params.run_centrifuge ) {
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format )
}
if ( params.run_metaphlan3 ) {
METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
}