mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 21:53:09 +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
|
@ -6,6 +6,12 @@
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"adapterremoval": {
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"adapterremoval": {
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"git_sha": "f0800157544a82ae222931764483331a81812012"
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"git_sha": "f0800157544a82ae222931764483331a81812012"
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},
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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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"cat/fastq": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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},
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@ -30,6 +36,9 @@
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"porechop": {
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"porechop": {
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"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
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"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
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},
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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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"untar": {
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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}
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}
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|
77
modules/nf-core/modules/bowtie2/align/main.nf
generated
Normal file
77
modules/nf-core/modules/bowtie2/align/main.nf
generated
Normal file
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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
Normal file
51
modules/nf-core/modules/bowtie2/align/meta.yml
generated
Normal file
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@ -0,0 +1,51 @@
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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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||||||
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type: file
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||||||
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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
Normal file
30
modules/nf-core/modules/bowtie2/build/main.nf
generated
Normal file
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@ -0,0 +1,30 @@
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process BOWTIE2_BUILD {
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||||||
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tag "$fasta"
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||||||
|
label 'process_high'
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||||||
|
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||||||
|
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
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||||||
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container "${ 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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||||||
|
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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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||||||
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path "versions.yml" , emit: versions
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||||||
|
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||||||
|
when:
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||||||
|
task.ext.when == null || task.ext.when
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||||||
|
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script:
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||||||
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def args = task.ext.args ?: ''
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||||||
|
"""
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||||||
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mkdir bowtie2
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||||||
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bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
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||||||
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cat <<-END_VERSIONS > versions.yml
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||||||
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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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}
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33
modules/nf-core/modules/bowtie2/build/meta.yml
generated
Normal file
33
modules/nf-core/modules/bowtie2/build/meta.yml
generated
Normal file
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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"
|
34
modules/nf-core/modules/samtools/flagstat/main.nf
generated
Normal file
34
modules/nf-core/modules/samtools/flagstat/main.nf
generated
Normal file
|
@ -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
|
||||||
|
"""
|
||||||
|
}
|
49
modules/nf-core/modules/samtools/flagstat/meta.yml
generated
Normal file
49
modules/nf-core/modules/samtools/flagstat/meta.yml
generated
Normal file
|
@ -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"
|
|
@ -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'
|
||||||
|
|
39
subworkflows/local/shortread_hostremoval.nf
Normal file
39
subworkflows/local/shortread_hostremoval.nf
Normal file
|
@ -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
|
||||||
|
}
|
||||||
|
|
|
@ -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
|
||||||
|
|
Loading…
Reference in a new issue