mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:13:09 +00:00
commit
6fecb3eeb7
14 changed files with 396 additions and 38 deletions
7
.github/workflows/ci.yml
vendored
7
.github/workflows/ci.yml
vendored
|
@ -29,8 +29,8 @@ jobs:
|
|||
- NXF_VER: ""
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NXF_EDGE: "1"
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parameters:
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- "--longread_clip false"
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- "--shortread_clip false"
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- "--perform_longread_clip false"
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- "--perform_shortread_clipmerge false"
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- "--shortread_clipmerge_tool fastp"
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- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
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- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
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||||
|
@ -39,6 +39,9 @@ jobs:
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- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
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- "--shortread_complexityfilter_tool bbduk"
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- "--shortread_complexityfilter_tool prinseq"
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- "--perform_runmerging"
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- "--perform_runmerging --shortread_clipmerge_mergepairs"
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- "--shortread_complexityfilter false --perform_shortread_hostremoval"
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steps:
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- name: Check out pipeline code
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|
|
|
@ -132,6 +132,24 @@ process {
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]
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}
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withName: BOWTIE2_BUILD {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/bowtie2/build" },
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mode: params.publish_dir_mode,
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pattern: '*.bt2'
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]
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}
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withName: BOWTIE2_ALIGN {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,bam}'
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]
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}
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withName: BBMAP_BBDUK {
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ext.args = [
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"entropy=${params.shortread_complexityfilter_entropy}",
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|
@ -161,9 +179,19 @@ process {
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]
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}
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withName: CAT_FASTQ {
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ext.prefix = { "${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/run_merging/" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_runmerged_reads
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]
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}
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withName: MALT_RUN {
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}" },
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mode: params.publish_dir_mode,
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|
@ -173,7 +201,7 @@ process {
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|||
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withName: KRAKEN2_KRAKEN2 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: params.publish_dir_mode,
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@ -182,12 +210,13 @@ process {
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}
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withName: METAPHLAN3 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/metaphlan3/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{biom,txt}'
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]
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CENTRIFUGE_CENTRIFUGE {
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|
|
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@ -28,7 +28,9 @@ params {
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run_malt = true
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run_metaphlan3 = true
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run_centrifuge = true
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shortread_clipmerge = true
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longread_clip = false
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shortread_complexityfilter = true
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perform_shortread_clipmerge = true
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perform_longread_clip = false
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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}
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|
|
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@ -9,6 +9,12 @@
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"bbmap/bbduk": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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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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|
|
77
modules/nf-core/modules/bowtie2/align/main.nf
generated
Normal file
77
modules/nf-core/modules/bowtie2/align/main.nf
generated
Normal file
|
@ -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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}
|
51
modules/nf-core/modules/bowtie2/align/meta.yml
generated
Normal file
51
modules/nf-core/modules/bowtie2/align/meta.yml
generated
Normal file
|
@ -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: |
|
||||
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
|
||||
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
|
||||
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:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
30
modules/nf-core/modules/bowtie2/build/main.nf
generated
Normal file
30
modules/nf-core/modules/bowtie2/build/main.nf
generated
Normal file
|
@ -0,0 +1,30 @@
|
|||
process BOWTIE2_BUILD {
|
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tag "$fasta"
|
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label 'process_high'
|
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|
||||
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
|
||||
container "${ 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
|
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"${task.process}":
|
||||
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
33
modules/nf-core/modules/bowtie2/build/meta.yml
generated
Normal file
33
modules/nf-core/modules/bowtie2/build/meta.yml
generated
Normal file
|
@ -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"
|
|
@ -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
|
||||
|
|
|
@ -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
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
@ -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'
|
||||
|
|
|
@ -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 )
|
||||
|
|
34
subworkflows/local/shortread_hostremoval.nf
Normal file
34
subworkflows/local/shortread_hostremoval.nf
Normal file
|
@ -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
|
||||
}
|
||||
|
|
@ -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
|
||||
|
|
Loading…
Reference in a new issue