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Start work on host removal

This commit is contained in:
James Fellows Yates 2022-04-03 07:58:40 +02:00
parent 1dfbcacf68
commit 482112bb42
10 changed files with 336 additions and 4 deletions

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@ -6,6 +6,12 @@
"adapterremoval": { "adapterremoval": {
"git_sha": "f0800157544a82ae222931764483331a81812012" "git_sha": "f0800157544a82ae222931764483331a81812012"
}, },
"bowtie2/align": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"bowtie2/build": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"cat/fastq": { "cat/fastq": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
}, },
@ -30,6 +36,9 @@
"porechop": { "porechop": {
"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046" "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
}, },
"samtools/flagstat": {
"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
},
"untar": { "untar": {
"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918" "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
} }

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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"

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@ -0,0 +1,34 @@
process SAMTOOLS_FLAGSTAT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
input:
tuple val(meta), path(bam), path(bai)
output:
tuple val(meta), path("*.flagstat"), emit: flagstat
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
samtools \\
flagstat \\
--threads ${task.cpus-1} \\
$bam \\
> ${bam}.flagstat
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}

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@ -0,0 +1,49 @@
name: samtools_flagstat
description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
keywords:
- stats
- mapping
- counts
- bam
- sam
- cram
tools:
- samtools:
description: |
SAMtools is a set of utilities for interacting with and post-processing
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
These files are generated as output by short read aligners like BWA.
homepage: http://www.htslib.org/
documentation: hhttp://www.htslib.org/doc/samtools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- bai:
type: file
description: Index for BAM/CRAM/SAM file
pattern: "*.{bai,crai,sai}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- flagstat:
type: file
description: File containing samtools flagstat output
pattern: "*.{flagstat}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@drpatelh"

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@ -65,6 +65,10 @@ params {
shortread_clipmerge_minlength = 15 shortread_clipmerge_minlength = 15
longread_clip = false longread_clip = false
// Host Removal
shortread_hostremoval_reference = null
shortread_hostremoval_index = null
// MALT // MALT
run_malt = false run_malt = false
malt_mode = 'BlastN' malt_mode = 'BlastN'

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@ -0,0 +1,39 @@
//
// Remove host reads via alignment and export off-target reads
//
include { BOWTIE2_ALIGN } from '../../../modules/nf-core/modules/bowtie2/align/main'
include { BOWTIE2_BUILD } from '../../../modules/nf-core/modules/bowtie2/build/main'
include { SAMTOOLS_VIEW } from '../../../modules/nf-core/modules/samtools/view/main'
include { SAMTOOLS_FASTQ } from '../../../modules/nf-core/modules/samtools/fastq/main'
include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/modules/samtools/flagstat/main'
workflow SHORTREAD_PREPROCESSING {
take:
reads // [ [ meta ], [ reads ] ]
reference // /path/to/fasta
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
if ( !params.shortread_hostremoval_index ) {
file( , checkIfExists: true )
BOWTIE2_BUILD ( reference )
ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
}
BOWTIE2_ALIGN ( reads, BOWTIE2_BUILD.out.index )
ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_FLAGSTAT.out.log )
SAMTOOLS_FLAGSTAT ( BOWTIE2_ALIGN.out.bam )
ch_versions = ch_versions.mix( SAMTOOLS_FLAGSTAT.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_FLAGSTAT.out.flagstat )
emit:
reads = BOWTIE2_ALIGN.out.fastq // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}

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@ -11,15 +11,21 @@ WorkflowTaxprofiler.initialise(params, log)
// TODO nf-core: Add all file path parameters for the pipeline to the list below // TODO nf-core: Add all file path parameters for the pipeline to the list below
// Check input path parameters to see if they exist // 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) } } for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
// Check mandatory parameters // Check mandatory parameters
if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' } if (params.databases ) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not except uncollapsed paired-reads. Pairs will be profiled as separate files." if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not except 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.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"
// TODO Add check if index but no reference exit 1
if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) } else { }
if (params.shortread_hostremoval_index) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
/* /*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CONFIG FILES CONFIG FILES