mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 06:53:10 +00:00
Start work on host removal
This commit is contained in:
parent
1dfbcacf68
commit
482112bb42
10 changed files with 336 additions and 4 deletions
11
modules.json
11
modules.json
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@ -6,6 +6,12 @@
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"adapterremoval": {
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"git_sha": "f0800157544a82ae222931764483331a81812012"
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},
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"bowtie2/align": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"bowtie2/build": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"cat/fastq": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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@ -30,9 +36,12 @@
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"porechop": {
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"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
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},
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"samtools/flagstat": {
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"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
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},
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"untar": {
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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}
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}
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}
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}
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}
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77
modules/nf-core/modules/bowtie2/align/main.nf
generated
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77
modules/nf-core/modules/bowtie2/align/main.nf
generated
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@ -0,0 +1,77 @@
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process BOWTIE2_ALIGN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
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'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }"
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input:
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tuple val(meta), path(reads)
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path index
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val save_unaligned
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output:
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tuple val(meta), path('*.bam') , emit: bam
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tuple val(meta), path('*.log') , emit: log
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tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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if (meta.single_end) {
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def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
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"""
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INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
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bowtie2 \\
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-x \$INDEX \\
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-U $reads \\
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--threads $task.cpus \\
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$unaligned \\
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$args \\
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2> ${prefix}.bowtie2.log \\
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| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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} else {
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def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
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"""
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INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
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bowtie2 \\
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-x \$INDEX \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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--threads $task.cpus \\
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$unaligned \\
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$args \\
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2> ${prefix}.bowtie2.log \\
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| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
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if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
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mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
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fi
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if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
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mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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}
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}
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51
modules/nf-core/modules/bowtie2/align/meta.yml
generated
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51
modules/nf-core/modules/bowtie2/align/meta.yml
generated
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name: bowtie2_align
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description: Align reads to a reference genome using bowtie2
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keywords:
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- align
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- fasta
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- genome
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- reference
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tools:
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- bowtie2:
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description: |
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Bowtie 2 is an ultrafast and memory-efficient tool for aligning
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sequencing reads to long reference sequences.
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homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
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documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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doi: 10.1038/nmeth.1923
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licence: ["GPL-3.0-or-later"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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type: file
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description: Bowtie2 genome index files
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pattern: "*.ebwt"
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output:
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- bam:
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type: file
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description: Output BAM file containing read alignments
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pattern: "*.{bam}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- fastq:
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type: file
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description: Unaligned FastQ files
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pattern: "*.fastq.gz"
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- log:
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type: file
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description: Aligment log
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pattern: "*.log"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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30
modules/nf-core/modules/bowtie2/build/main.nf
generated
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30
modules/nf-core/modules/bowtie2/build/main.nf
generated
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process BOWTIE2_BUILD {
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tag "$fasta"
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label 'process_high'
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conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
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'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
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input:
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path fasta
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output:
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path 'bowtie2' , emit: index
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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mkdir bowtie2
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bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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33
modules/nf-core/modules/bowtie2/build/meta.yml
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33
modules/nf-core/modules/bowtie2/build/meta.yml
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name: bowtie2_build
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description: Builds bowtie index for reference genome
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keywords:
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- build
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- index
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- fasta
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- genome
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- reference
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tools:
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- bowtie2:
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description: |
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Bowtie 2 is an ultrafast and memory-efficient tool for aligning
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sequencing reads to long reference sequences.
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homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
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documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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doi: 10.1038/nmeth.1923
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licence: ["GPL-3.0-or-later"]
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input:
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- fasta:
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type: file
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description: Input genome fasta file
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output:
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- index:
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type: file
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description: Bowtie2 genome index files
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pattern: "*.bt2"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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34
modules/nf-core/modules/samtools/flagstat/main.nf
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34
modules/nf-core/modules/samtools/flagstat/main.nf
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process SAMTOOLS_FLAGSTAT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
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'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
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input:
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tuple val(meta), path(bam), path(bai)
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output:
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tuple val(meta), path("*.flagstat"), emit: flagstat
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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samtools \\
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flagstat \\
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--threads ${task.cpus-1} \\
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$bam \\
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> ${bam}.flagstat
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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49
modules/nf-core/modules/samtools/flagstat/meta.yml
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49
modules/nf-core/modules/samtools/flagstat/meta.yml
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name: samtools_flagstat
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description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
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keywords:
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- stats
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- mapping
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- counts
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- bam
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- sam
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- cram
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tools:
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- samtools:
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description: |
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SAMtools is a set of utilities for interacting with and post-processing
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short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
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These files are generated as output by short read aligners like BWA.
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homepage: http://www.htslib.org/
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documentation: hhttp://www.htslib.org/doc/samtools.html
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doi: 10.1093/bioinformatics/btp352
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- bai:
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type: file
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description: Index for BAM/CRAM/SAM file
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pattern: "*.{bai,crai,sai}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- flagstat:
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type: file
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description: File containing samtools flagstat output
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pattern: "*.{flagstat}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@drpatelh"
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shortread_clipmerge_minlength = 15
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longread_clip = false
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// Host Removal
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shortread_hostremoval_reference = null
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shortread_hostremoval_index = null
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// MALT
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run_malt = false
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malt_mode = 'BlastN'
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39
subworkflows/local/shortread_hostremoval.nf
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39
subworkflows/local/shortread_hostremoval.nf
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//
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// Remove host reads via alignment and export off-target reads
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//
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include { BOWTIE2_ALIGN } from '../../../modules/nf-core/modules/bowtie2/align/main'
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include { BOWTIE2_BUILD } from '../../../modules/nf-core/modules/bowtie2/build/main'
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include { SAMTOOLS_VIEW } from '../../../modules/nf-core/modules/samtools/view/main'
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include { SAMTOOLS_FASTQ } from '../../../modules/nf-core/modules/samtools/fastq/main'
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include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/modules/samtools/flagstat/main'
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workflow SHORTREAD_PREPROCESSING {
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take:
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reads // [ [ meta ], [ reads ] ]
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reference // /path/to/fasta
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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if ( !params.shortread_hostremoval_index ) {
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file( , checkIfExists: true )
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BOWTIE2_BUILD ( reference )
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ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
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}
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BOWTIE2_ALIGN ( reads, BOWTIE2_BUILD.out.index )
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ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_FLAGSTAT.out.log )
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SAMTOOLS_FLAGSTAT ( BOWTIE2_ALIGN.out.bam )
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ch_versions = ch_versions.mix( SAMTOOLS_FLAGSTAT.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_FLAGSTAT.out.flagstat )
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emit:
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reads = BOWTIE2_ALIGN.out.fastq // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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@ -11,15 +11,21 @@ WorkflowTaxprofiler.initialise(params, log)
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// TODO nf-core: Add all file path parameters for the pipeline to the list below
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// Check input path parameters to see if they exist
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def checkPathParamList = [ params.input, params.databases, params.multiqc_config ]
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def checkPathParamList = [ params.input, params.databases, params.shortread_hostremoval_reference,
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params.shortread_hostremoval_index, params.multiqc_config
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]
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for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
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// Check mandatory parameters
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if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
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if (params.databases ) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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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."
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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"
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// TODO Add check if index but no reference exit 1
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if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) } else { }
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if (params.shortread_hostremoval_index) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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CONFIG FILES
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