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Merge branch 'dev' into hostremoval

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James A. Fellows Yates 2022-04-13 13:59:51 +02:00 committed by GitHub
commit 70f94603b0
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10 changed files with 111 additions and 171 deletions
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6
.github/workflows/ci.yml vendored
View file

@ -29,8 +29,8 @@ jobs:
- NXF_VER: ""
NXF_EDGE: "1"
parameters:
- "--longread_clip false"
- "--shortread_clip false"
- "--perform_longread_clip false"
- "--perform_shortread_clipmerge false"
- "--shortread_clipmerge_tool fastp"
- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
@ -39,6 +39,8 @@ jobs:
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
- "--shortread_complexityfilter_tool bbduk"
- "--shortread_complexityfilter_tool prinseq"
- "--perform_runmerging"
- "--perform_runmerging --shortread_clipmerge_mergepairs"
- "--shortread_complexityfilter false --shortread_hostremoval"
steps:

17
conf/modules.config
View file

@ -179,9 +179,19 @@ process {
]
}
withName: CAT_FASTQ {
ext.prefix = { "${meta.id}" }
publishDir = [
path: { "${params.outdir}/run_merging/" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_runmerged_reads
]
}
withName: MALT_RUN {
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}" },
mode: params.publish_dir_mode,
@ -191,7 +201,7 @@ process {
withName: KRAKEN2_KRAKEN2 {
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}" },
mode: params.publish_dir_mode,
@ -200,12 +210,13 @@ process {
}
withName: METAPHLAN3 {
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/metaphlan3/${meta.db_name}" },
mode: params.publish_dir_mode,
pattern: '*.{biom,txt}'
]
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
}
withName: CENTRIFUGE_CENTRIFUGE {

19
conf/test.config
View file

@ -22,16 +22,15 @@ params {
// Input data
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
run_kraken2 = true
run_malt = true
run_metaphlan3 = true
run_centrifuge = true
shortread_clipmerge = true
longread_clip = false
shortread_complexityfilter = true
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
run_kraken2 = true
run_malt = true
run_metaphlan3 = true
run_centrifuge = true
perform_shortread_clipmerge = true
perform_longread_clip = false
perform_shortread_complexityfilter = true
shortread_hostremoval = true
shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
}

10
nextflow.config
View file

@ -55,7 +55,7 @@ params {
databases = null
// FASTQ preprocessing
shortread_clipmerge = false
perform_shortread_clipmerge = false
shortread_clipmerge_tool = 'fastp'
shortread_clipmerge_skipadaptertrim = false
shortread_clipmerge_mergepairs = false
@ -63,11 +63,11 @@ params {
shortread_clipmerge_adapter1 = null
shortread_clipmerge_adapter2 = null
shortread_clipmerge_minlength = 15
longread_clip = false
perform_longread_clip = false
save_preprocessed_reads = false
// Complexity filtering
shortread_complexityfilter = false
perform_shortread_complexityfilter = false
shortread_complexityfilter_tool = 'bbduk'
shortread_complexityfilter_entropy = 0.3
shortread_complexityfilter_bbduk_windowsize = 50
@ -76,6 +76,9 @@ params {
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
save_complexityfiltered_reads = false
// run merging
perform_runmerging = false
save_runmerged_reads = false
// Host Removal
shortread_hostremoval = false
@ -94,6 +97,7 @@ params {
centrifuge_save_unaligned = false
centrifuge_save_aligned = false
centrifuge_sam_format = false
// metaphlan3
run_metaphlan3 = false
}

30
nextflow_schema.json
View file

@ -262,15 +262,9 @@
"type": "string",
"default": "None"
},
"shortread_clipmerge": {
"type": "boolean"
},
"shortread_clipmerge_excludeunmerged": {
"type": "boolean"
},
"longread_clip": {
"type": "boolean"
},
"run_malt": {
"type": "boolean"
},
@ -321,8 +315,7 @@
"default": 15
},
"save_preprocessed_reads": {
"type": "boolean",
"default": false
"type": "boolean"
},
"shortread_complexityfilter_tool": {
"type": "string",
@ -335,9 +328,6 @@
"shortread_complexityfilter_bbduk_mask": {
"type": "boolean"
},
"shortread_complexityfilter": {
"type": "boolean"
},
"shortread_complexityfilter_entropy": {
"type": "number",
"default": 0.3
@ -352,8 +342,22 @@
"default": 0.5
},
"save_complexityfiltered_reads": {
"type": "boolean",
"default": false
"type": "boolean"
},
"save_runmerged_reads": {
"type": "boolean"
},
"perform_shortread_clipmerge": {
"type": "boolean"
},
"perform_longread_clip": {
"type": "boolean"
},
"perform_shortread_complexityfilter": {
"type": "boolean"
},
"perform_runmerging": {
"type": "boolean"
},
"shortread_hostremoval": {
"type": "boolean"

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

@ -1,61 +0,0 @@
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
View file

@ -1,66 +0,0 @@
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"

13
subworkflows/local/profiling.nf
View file

@ -9,8 +9,7 @@ include { METAPHLAN3 } from '../../modules/nf-core/modules/meta
workflow PROFILING {
take:
shortreads // [ [ meta ], [ reads ] ]
longreads // [ [ meta ], [ reads ] ]
reads // [ [ meta ], [ reads ] ]
databases // [ [ meta ], path ]
main:
@ -22,8 +21,14 @@ workflow PROFILING {
*/
// e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
ch_input_for_profiling = shortreads
.mix( longreads )
ch_input_for_profiling = reads
.map {
meta, reads ->
def meta_new = meta.clone()
pairtype = meta_new['single_end'] ? '_se' : '_pe'
meta_new['id'] = meta_new['id'] + pairtype
[meta_new, reads]
}
.combine(databases)
.branch {
malt: it[2]['tool'] == 'malt'

4
subworkflows/local/shortread_fastp.nf
View file

@ -28,8 +28,8 @@ workflow SHORTREAD_FASTP {
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
meta_new['single_end'] = true
[ meta_new, [ reads ].flatten() ]
}
ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )

56
workflows/taxprofiler.nf
View file

@ -111,14 +111,14 @@ workflow TAXPROFILER {
/*
SUBWORKFLOW: PERFORM PREPROCESSING
*/
if ( params.shortread_clipmerge ) {
if ( params.perform_shortread_clipmerge ) {
ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
} else {
ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
}
if ( params.longread_clip ) {
if ( params.perform_longread_clip ) {
ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
.map { it -> [ it[0], [it[1]] ] }
ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
@ -130,7 +130,7 @@ workflow TAXPROFILER {
SUBWORKFLOW: COMPLEXITY FILTERING
*/
if ( params.shortread_complexityfilter ) {
if ( params.perform_shortread_complexityfilter ) {
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
} else {
ch_shortreads_filtered = ch_shortreads_preprocessed
@ -147,11 +147,48 @@ workflow TAXPROFILER {
ch_shortreads_hostremoved = ch_shortreads_filtered
}
*/
if ( params.perform_runmerging ) {
ch_reads_for_cat_branch = ch_shortreads_hostremoved
.mix( ch_longreads_preprocessed )
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new.remove('run_accession')
[ meta_new, reads ]
}
.groupTuple()
.map {
meta, reads ->
[ meta, reads.flatten() ]
}
.branch {
meta, reads ->
// we can't concatenate files if there is not a second run, we branch
// here to separate them out, and mix back in after for efficiency
cat: ( meta.single_end && reads.size() > 1 ) || ( !meta.single_end && reads.size() > 2 )
skip: true
}
ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat_branch.cat ).reads
.mix( ch_reads_for_cat_branch.skip )
.map {
meta, reads ->
[ meta, [ reads ].flatten() ]
}
} else {
ch_reads_runmerged = ch_shortreads_hostremoved
.mix( ch_longreads_preprocessed )
}
/*
SUBWORKFLOW: PROFILING
*/
PROFILING ( ch_shortreads_hostremoved, ch_longreads_preprocessed, DB_CHECK.out.dbs )
PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
ch_versions = ch_versions.mix( PROFILING.out.versions )
/*
@ -173,23 +210,28 @@ workflow TAXPROFILER {
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
if (params.shortread_clipmerge) {
if (params.perform_shortread_clipmerge) {
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
}
if (params.longread_clip) {
if (params.perform_longread_clip) {
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
}
if (params.shortread_complexityfilter){
if (params.perform_shortread_complexityfilter){
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
}
if (params.shortread_hostremoval) {
ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
}
if (params.perform_runmerging){
ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
}
ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc )