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Merge pull request #86 from nf-core/support-aligned-reads

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Add working read alignment output for MALT/Kraken2/Centrifuge/DIAMOND
This commit is contained in:
James A. Fellows Yates 2022-06-13 11:23:34 +02:00 committed by GitHub
commit 3dcda7446b
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GPG key ID: 4AEE18F83AFDEB23
12 changed files with 155 additions and 60 deletions
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4
conf/modules.config
View file

@ -289,7 +289,7 @@ process {
publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}" },
mode: params.publish_dir_mode,
pattern: '*.{txt}'
pattern: '*.{txt,report,fastq.gz}'
]
}
@ -307,7 +307,7 @@ process {
publishDir = [
path: { "${params.outdir}/centrifuge/${meta.db_name}" },
mode: params.publish_dir_mode,
pattern: '*.txt'
pattern: '*.{txt,sam,gz}'
]
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }

7
conf/test.config
View file

@ -37,10 +37,17 @@ params {
run_metaphlan3 = true
run_centrifuge = true
run_diamond = true
malt_save_reads = true
kraken2_save_reads = true
centrifuge_save_reads = true
diamond_save_reads = true
}
process {
withName: MALT_RUN {
maxForks = 1
}
withName: MEGAN_RMA2INFO {
maxForks = 1
}
}

4
modules.json
View file

@ -28,7 +28,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"diamond/blastx": {
"git_sha": "42564565b934eeb2449e35ec97ed13ff2a67f1de"
"git_sha": "bd3bfe0817246082525ab93707976676b1fe208b"
},
"fastp": {
"git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"
@ -46,7 +46,7 @@
"git_sha": "538dbac98ba9c8f799536cd5a617195501439457"
},
"kraken2/kraken2": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
"git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
},
"malt/run": {
"git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"

33
modules/nf-core/modules/diamond/blastx/main.nf generated
View file

@ -2,21 +2,26 @@ process DIAMOND_BLASTX {
tag "$meta.id"
label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a
// singularity version higher than this at the current time.
conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
input:
tuple val(meta), path(fasta)
path db
val outext
val out_ext
val blast_columns
output:
tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
path "versions.yml" , emit: versions
tuple val(meta), path('*.blast'), optional: true, emit: blast
tuple val(meta), path('*.xml') , optional: true, emit: xml
tuple val(meta), path('*.txt') , optional: true, emit: txt
tuple val(meta), path('*.daa') , optional: true, emit: daa
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.tsv') , optional: true, emit: tsv
tuple val(meta), path('*.paf') , optional: true, emit: paf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -24,7 +29,8 @@ process DIAMOND_BLASTX {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
switch ( outext ) {
def columns = blast_columns ? "${blast_columns}" : ''
switch ( out_ext ) {
case "blast": outfmt = 0; break
case "xml": outfmt = 5; break
case "txt": outfmt = 6; break
@ -32,6 +38,11 @@ process DIAMOND_BLASTX {
case "sam": outfmt = 101; break
case "tsv": outfmt = 102; break
case "paf": outfmt = 103; break
default:
outfmt = '6';
out_ext = 'txt';
log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
break
}
"""
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
@ -41,9 +52,9 @@ process DIAMOND_BLASTX {
--threads $task.cpus \\
--db \$DB \\
--query $fasta \\
--outfmt ${outfmt} \\
--outfmt ${outfmt} ${columns} \\
$args \\
--out ${prefix}.${outext}
--out ${prefix}.${out_ext}
cat <<-END_VERSIONS > versions.yml
"${task.process}":

30
modules/nf-core/modules/diamond/blastx/meta.yml generated
View file

@ -28,7 +28,7 @@ input:
type: directory
description: Directory containing the nucelotide blast database
pattern: "*"
- outext:
- out_ext:
type: string
description: |
Specify the type of output file to be generated. `blast` corresponds to
@ -38,10 +38,34 @@ input:
pattern: "blast|xml|txt|daa|sam|tsv|paf"
output:
- blast:
type: file
description: File containing blastp hits
pattern: "*.{blast}"
- xml:
type: file
description: File containing blastp hits
pattern: "*.{xml}"
- txt:
type: file
description: File containing blastx hits
pattern: "*.{blastx.txt}"
description: File containing hits in tabular BLAST format.
pattern: "*.{txt}"
- daa:
type: file
description: File containing hits DAA format
pattern: "*.{daa}"
- sam:
type: file
description: File containing aligned reads in SAM format
pattern: "*.{sam}"
- tsv:
type: file
description: Tab separated file containing taxonomic classification of hits
pattern: "*.{tsv}"
- paf:
type: file
description: File containing aligned reads in pairwise mapping format format
pattern: "*.{paf}"
- versions:
type: file
description: File containing software versions

23
modules/nf-core/modules/kraken2/kraken2/main.nf generated
View file

@ -10,12 +10,15 @@ process KRAKEN2_KRAKEN2 {
input:
tuple val(meta), path(reads)
path db
val save_output_fastqs
val save_reads_assignment
output:
tuple val(meta), path('*classified*') , emit: classified
tuple val(meta), path('*unclassified*'), emit: unclassified
tuple val(meta), path('*report.txt') , emit: txt
path "versions.yml" , emit: versions
tuple val(meta), path('*classified*') , optional:true, emit: classified_reads_fastq
tuple val(meta), path('*unclassified*') , optional:true, emit: unclassified_reads_fastq
tuple val(meta), path('*classifiedreads*'), optional:true, emit: classified_reads_assignment
tuple val(meta), path('*report.txt') , emit: report
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -26,19 +29,25 @@ process KRAKEN2_KRAKEN2 {
def paired = meta.single_end ? "" : "--paired"
def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq"
def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
def classified_command = save_output_fastqs ? "--classified-out ${classified}" : ""
def unclassified_command = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
def readclassification_command = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : ""
def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
"""
kraken2 \\
--db $db \\
--threads $task.cpus \\
--unclassified-out $unclassified \\
--classified-out $classified \\
--report ${prefix}.kraken2.report.txt \\
--gzip-compressed \\
$unclassified_command \\
$classified_command \\
$readclassification_command \\
$paired \\
$args \\
$reads
pigz -p $task.cpus *.fastq
$compress_reads_command
cat <<-END_VERSIONS > versions.yml
"${task.process}":

25
modules/nf-core/modules/kraken2/kraken2/meta.yml generated
View file

@ -27,25 +27,40 @@ input:
- db:
type: directory
description: Kraken2 database
- save_output_fastqs:
type: boolean
description: |
If true, optional commands are added to save classified and unclassified reads
as fastq files
- save_reads_assignment:
type: boolean
description: |
If true, an optional command is added to save a file reporting the taxonomic
classification of each input read
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- classified:
- classified_reads_fastq:
type: file
description: |
Reads classified to belong to any of the taxa
Reads classified as belonging to any of the taxa
on the Kraken2 database.
pattern: "*{fastq.gz}"
- unclassified:
- unclassified_reads_fastq:
type: file
description: |
Reads not classified to belong to any of the taxa
Reads not classified to any of the taxa
on the Kraken2 database.
pattern: "*{fastq.gz}"
- txt:
- classified_reads_assignment:
type: file
description: |
Kraken2 output file indicating the taxonomic assignment of
each input read
- report:
type: file
description: |
Kraken2 report containing stats about classified

16
nextflow.config
View file

@ -102,16 +102,17 @@ params {
// MALT
run_malt = false
malt_mode = 'BlastN'
malt_generatemegansummary = false
malt_generate_megansummary = false
malt_save_reads = false
// kraken2
run_kraken2 = false
run_kraken2 = false
kraken2_save_reads = false
kraken2_save_readclassification = false
// centrifuge
run_centrifuge = false
centrifuge_save_unaligned = false
centrifuge_save_aligned = false
centrifuge_sam_format = false
centrifuge_save_reads = false
// metaphlan3
run_metaphlan3 = false
@ -122,7 +123,8 @@ params {
// diamond
run_diamond = false
diamond_output_format = 'txt'
diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently
diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated!
}
// Load base.config by default for all pipelines
@ -194,7 +196,7 @@ profiles {
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
test_nopreprocessing { includeConfig 'conf/test_preprocessing.config' }
test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
}
// Load igenomes.config if required

26
nextflow_schema.json
View file

@ -278,15 +278,6 @@
"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"
@ -386,7 +377,7 @@
"run_kaiju": {
"type": "boolean"
},
"malt_generatemegansummary": {
"malt_generate_megansummary": {
"type": "boolean"
},
"kaiju_taxon_name": {
@ -427,6 +418,21 @@
"longread_qc_target_bases": {
"type": "integer",
"default": 500000000
},
"malt_save_reads": {
"type": "boolean"
},
"kraken2_save_reads": {
"type": "boolean"
},
"kraken2_save_readclassification": {
"type": "boolean"
},
"centrifuge_save_reads": {
"type": "boolean"
},
"diamond_save_reads": {
"type": "boolean"
}
}
}

2
subworkflows/local/longread_preprocessing.nf
View file

@ -48,7 +48,7 @@ workflow LONGREAD_PREPROCESSING {
}
FASTQC_PROCESSED ( ch_processed_reads.dump(tag: "filtlong") )
FASTQC_PROCESSED ( ch_processed_reads )
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
emit:

43
subworkflows/local/profiling.nf
View file

@ -61,14 +61,29 @@ workflow PROFILING {
// MALT: We groupTuple to have all samples in one channel for MALT as database
// loading takes a long time, so we only want to run it once per database
// TODO document somewhere we only accept illumina short reads for MALT?
ch_input_for_malt = ch_input_for_profiling.malt
.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
.map {
it ->
def temp_meta = [ id: it[2]['db_name']] + it[2]
def db = it[3]
[ temp_meta, it[1], db ]
meta, reads, db_meta, db ->
// Reset entire input meta for MALT to just database name,
// as we don't run run on a per-sample basis due to huge datbaases
// so all samples are in one run and so sample-specific metadata
// unnecessary. Set as database name to prevent `null` job ID and prefix.
def temp_meta = [ id: meta['db_name'] ]
// Extend database parameters to specify whether to save alignments or not
def new_db_meta = db_meta.clone()
def sam_format = params.malt_save_reads ? ' --alignments ./ -za false' : ""
new_db_meta['db_params'] = db_meta['db_params'] + sam_format
// Combine reduced sample metadata with updated database parameters metadata,
// make sure id is db_name for publishing purposes.
def new_meta = temp_meta + new_db_meta
new_meta['id'] = new_meta['db_name']
[ new_meta, reads, db ]
}
.groupTuple(by: [0,2])
.multiMap {
@ -92,7 +107,7 @@ workflow PROFILING {
[ meta_new, rma ]
}
MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generatemegansummary )
MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generate_megansummary )
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
@ -108,10 +123,10 @@ workflow PROFILING {
db: it[3]
}
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.txt )
ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
}
@ -128,7 +143,7 @@ workflow PROFILING {
db: it[3]
}
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format )
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads )
CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
@ -180,9 +195,13 @@ workflow PROFILING {
db: it[3]
}
DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format )
// diamond only accepts single output file specification, therefore
// this will replace output file!
ch_diamond_reads_format = params.diamond_save_reads ? 'sam' : params.diamond_output_format
DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, ch_diamond_reads_format , [] )
ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.output )
ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.tsv )
}

2
workflows/taxprofiler.nf
View file

@ -33,6 +33,8 @@ if (params.hostremoval_reference ) { ch_reference = file(params.hostre
if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = file(params.shortread_hostremoval_index ) } else { ch_shortread_reference_index = [] }
if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] }
if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. As --diamond_save_reads supplied, only aligned reads in SAM format will be produced, no taxonomic profiles will be available."
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CONFIG FILES