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Merge pull request #54 from nf-core/dev

Get upstream changes
This commit is contained in:
James A. Fellows Yates 2022-04-16 06:17:33 +02:00 committed by GitHub
commit 6fecb3eeb7
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GPG key ID: 4AEE18F83AFDEB23
14 changed files with 396 additions and 38 deletions

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@ -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 +39,9 @@ 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 --perform_shortread_hostremoval"
steps:
- name: Check out pipeline code

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@ -132,6 +132,24 @@ process {
]
}
withName: BOWTIE2_BUILD {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/bowtie2/build" },
mode: params.publish_dir_mode,
pattern: '*.bt2'
]
}
withName: BOWTIE2_ALIGN {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,bam}'
]
}
withName: BBMAP_BBDUK {
ext.args = [
"entropy=${params.shortread_complexityfilter_entropy}",
@ -161,9 +179,19 @@ process {
]
}
withName: CAT_FASTQ {
ext.prefix = { "${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,
@ -173,7 +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/${meta.db_name}" },
mode: params.publish_dir_mode,
@ -182,12 +210,13 @@ process {
}
withName: METAPHLAN3 {
ext.args = { "${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 {

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@ -28,7 +28,9 @@ params {
run_malt = true
run_metaphlan3 = true
run_centrifuge = true
shortread_clipmerge = true
longread_clip = false
shortread_complexityfilter = true
perform_shortread_clipmerge = true
perform_longread_clip = false
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
}

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@ -9,6 +9,12 @@
"bbmap/bbduk": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"bowtie2/align": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"bowtie2/build": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"cat/fastq": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},

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@ -0,0 +1,77 @@
process BOWTIE2_ALIGN {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }"
input:
tuple val(meta), path(reads)
path index
val save_unaligned
output:
tuple val(meta), path('*.bam') , emit: bam
tuple val(meta), path('*.log') , emit: log
tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 \\
-x \$INDEX \\
-U $reads \\
--threads $task.cpus \\
$unaligned \\
$args \\
2> ${prefix}.bowtie2.log \\
| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
} else {
def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 \\
-x \$INDEX \\
-1 ${reads[0]} \\
-2 ${reads[1]} \\
--threads $task.cpus \\
$unaligned \\
$args \\
2> ${prefix}.bowtie2.log \\
| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
fi
if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
}
}

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@ -0,0 +1,51 @@
name: bowtie2_align
description: Align reads to a reference genome using bowtie2
keywords:
- align
- fasta
- genome
- reference
tools:
- bowtie2:
description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
licence: ["GPL-3.0-or-later"]
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.
- index:
type: file
description: Bowtie2 genome index files
pattern: "*.ebwt"
output:
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fastq:
type: file
description: Unaligned FastQ files
pattern: "*.fastq.gz"
- log:
type: file
description: Aligment log
pattern: "*.log"
authors:
- "@joseespinosa"
- "@drpatelh"

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@ -0,0 +1,30 @@
process BOWTIE2_BUILD {
tag "$fasta"
label 'process_high'
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
input:
path fasta
output:
path 'bowtie2' , emit: index
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
mkdir bowtie2
bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
END_VERSIONS
"""
}

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@ -0,0 +1,33 @@
name: bowtie2_build
description: Builds bowtie index for reference genome
keywords:
- build
- index
- fasta
- genome
- reference
tools:
- bowtie2:
description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
licence: ["GPL-3.0-or-later"]
input:
- fasta:
type: file
description: Input genome fasta file
output:
- index:
type: file
description: Bowtie2 genome index files
pattern: "*.bt2"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"

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 +76,14 @@ params {
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
save_complexityfiltered_reads = false
// run merging
perform_runmerging = false
save_runmerged_reads = false
// Host Removal
perform_shortread_hostremoval = false
shortread_hostremoval_reference = null
shortread_hostremoval_index = null
// MALT
run_malt = false

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@ -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 +342,33 @@
"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"
},
"perform_shortread_hostremoval": {
"type": "boolean"
},
"shortread_hostremoval_reference": {
"type": "string",
"default": null
},
"shortread_hostremoval_index": {
"type": "string",
"default": null
}
}
}

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@ -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:
@ -23,8 +22,14 @@ 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'

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 )

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@ -0,0 +1,34 @@
//
// Remove host reads via alignment and export off-target reads
//
include { BOWTIE2_BUILD } from '../../modules/nf-core/modules/bowtie2/build/main'
include { BOWTIE2_ALIGN } from '../../modules/nf-core/modules/bowtie2/align/main'
workflow SHORTREAD_HOSTREMOVAL {
take:
reads // [ [ meta ], [ reads ] ]
reference // /path/to/fasta
index // /path/to/index
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
if ( !params.shortread_hostremoval_index ) {
ch_bowtie2_index = BOWTIE2_BUILD ( reference ).index
ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
} else {
ch_bowtie2_index = index.first()
}
BOWTIE2_ALIGN ( reads, ch_bowtie2_index, true )
ch_versions = ch_versions.mix( BOWTIE2_ALIGN.out.versions.first() )
ch_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
emit:
reads = BOWTIE2_ALIGN.out.fastq // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}

View file

@ -11,7 +11,9 @@ WorkflowTaxprofiler.initialise(params, log)
// TODO nf-core: Add all file path parameters for the pipeline to the list below
// Check input path parameters to see if they exist
def checkPathParamList = [ params.input, params.databases, params.multiqc_config ]
def checkPathParamList = [ params.input, params.databases, params.shortread_hostremoval_reference,
params.shortread_hostremoval_index, params.multiqc_config
]
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
// Check mandatory parameters
@ -20,6 +22,12 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, '
if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) }
if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CONFIG FILES
@ -43,6 +51,7 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { DB_CHECK } from '../subworkflows/local/db_check'
include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_hostremoval'
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
include { PROFILING } from '../subworkflows/local/profiling'
@ -101,16 +110,17 @@ 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())
} else {
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
}
@ -119,17 +129,63 @@ 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
}
/*
SUBWORKFLOW: HOST REMOVAL
*/
if ( params.perform_shortread_hostremoval ) {
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first())
} else {
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_filtered, ch_longreads_preprocessed, DB_CHECK.out.dbs )
PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
ch_versions = ch_versions.mix( PROFILING.out.versions )
/*
@ -151,21 +207,30 @@ 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.perform_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 )
// TODO create multiQC module for metaphlan