mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 06:33:09 +00:00
Add working output for Kraken2/Centrifuge/DIAMOND
This commit is contained in:
parent
e7b54801ed
commit
87a1d80519
11 changed files with 181 additions and 65 deletions
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@ -271,7 +271,7 @@ process {
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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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pattern: '*.{txt}'
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pattern: '*.{txt,report,fastq.gz}'
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]
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}
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@ -289,7 +289,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/centrifuge/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.txt'
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pattern: '*.{txt,sam,gz}'
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]
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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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@ -36,6 +36,10 @@ params {
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run_metaphlan3 = true
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run_centrifuge = true
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run_diamond = true
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malt_save_reads = true
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kraken2_save_reads = true
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centrifuge_save_reads = true
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diamond_save_reads = true
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}
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process {
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@ -28,7 +28,7 @@
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"diamond/blastx": {
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"git_sha": "42564565b934eeb2449e35ec97ed13ff2a67f1de"
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"git_sha": "bd3bfe0817246082525ab93707976676b1fe208b"
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},
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"fastp": {
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"git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"
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@ -43,7 +43,7 @@
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"git_sha": "538dbac98ba9c8f799536cd5a617195501439457"
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},
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"kraken2/kraken2": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
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},
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"malt/run": {
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"git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
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@ -80,4 +80,4 @@
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}
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}
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}
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}
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}
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33
modules/nf-core/modules/diamond/blastx/main.nf
generated
33
modules/nf-core/modules/diamond/blastx/main.nf
generated
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@ -2,21 +2,26 @@ process DIAMOND_BLASTX {
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tag "$meta.id"
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label 'process_medium'
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// Dimaond is limited to v2.0.9 because there is not a
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// singularity version higher than this at the current time.
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conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
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conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
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'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
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'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
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'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
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input:
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tuple val(meta), path(fasta)
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path db
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val outext
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val out_ext
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val blast_columns
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output:
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tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
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path "versions.yml" , emit: versions
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tuple val(meta), path('*.blast'), optional: true, emit: blast
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tuple val(meta), path('*.xml') , optional: true, emit: xml
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tuple val(meta), path('*.txt') , optional: true, emit: txt
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tuple val(meta), path('*.daa') , optional: true, emit: daa
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tuple val(meta), path('*.sam') , optional: true, emit: sam
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tuple val(meta), path('*.tsv') , optional: true, emit: tsv
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tuple val(meta), path('*.paf') , optional: true, emit: paf
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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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@ -24,7 +29,8 @@ process DIAMOND_BLASTX {
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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switch ( outext ) {
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def columns = blast_columns ? "${blast_columns}" : ''
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switch ( out_ext ) {
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case "blast": outfmt = 0; break
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case "xml": outfmt = 5; break
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case "txt": outfmt = 6; break
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@ -32,6 +38,11 @@ process DIAMOND_BLASTX {
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case "sam": outfmt = 101; break
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case "tsv": outfmt = 102; break
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case "paf": outfmt = 103; break
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default:
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outfmt = '6';
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out_ext = 'txt';
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log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
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break
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}
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"""
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DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
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@ -41,9 +52,9 @@ process DIAMOND_BLASTX {
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--threads $task.cpus \\
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--db \$DB \\
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--query $fasta \\
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--outfmt ${outfmt} \\
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--outfmt ${outfmt} ${columns} \\
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$args \\
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--out ${prefix}.${outext}
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--out ${prefix}.${out_ext}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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30
modules/nf-core/modules/diamond/blastx/meta.yml
generated
30
modules/nf-core/modules/diamond/blastx/meta.yml
generated
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@ -28,7 +28,7 @@ input:
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type: directory
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description: Directory containing the nucelotide blast database
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pattern: "*"
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- outext:
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- out_ext:
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type: string
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description: |
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Specify the type of output file to be generated. `blast` corresponds to
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@ -38,10 +38,34 @@ input:
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pattern: "blast|xml|txt|daa|sam|tsv|paf"
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output:
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- blast:
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type: file
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description: File containing blastp hits
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pattern: "*.{blast}"
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- xml:
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type: file
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description: File containing blastp hits
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pattern: "*.{xml}"
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- txt:
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type: file
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description: File containing blastx hits
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pattern: "*.{blastx.txt}"
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description: File containing hits in tabular BLAST format.
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pattern: "*.{txt}"
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- daa:
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type: file
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description: File containing hits DAA format
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pattern: "*.{daa}"
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- sam:
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type: file
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description: File containing aligned reads in SAM format
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pattern: "*.{sam}"
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- tsv:
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type: file
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description: Tab separated file containing taxonomic classification of hits
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pattern: "*.{tsv}"
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- paf:
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type: file
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description: File containing aligned reads in pairwise mapping format format
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pattern: "*.{paf}"
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- versions:
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type: file
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description: File containing software versions
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23
modules/nf-core/modules/kraken2/kraken2/main.nf
generated
23
modules/nf-core/modules/kraken2/kraken2/main.nf
generated
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@ -10,12 +10,15 @@ process KRAKEN2_KRAKEN2 {
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input:
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tuple val(meta), path(reads)
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path db
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val save_output_fastqs
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val save_reads_assignment
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output:
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tuple val(meta), path('*classified*') , emit: classified
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tuple val(meta), path('*unclassified*'), emit: unclassified
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tuple val(meta), path('*report.txt') , emit: txt
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path "versions.yml" , emit: versions
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tuple val(meta), path('*classified*') , optional:true, emit: classified_reads_fastq
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tuple val(meta), path('*unclassified*') , optional:true, emit: unclassified_reads_fastq
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tuple val(meta), path('*classifiedreads*'), optional:true, emit: classified_reads_assignment
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tuple val(meta), path('*report.txt') , emit: report
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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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@ -26,19 +29,25 @@ process KRAKEN2_KRAKEN2 {
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def paired = meta.single_end ? "" : "--paired"
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def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq"
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def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
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def classified_command = save_output_fastqs ? "--classified-out ${classified}" : ""
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def unclassified_command = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
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def readclassification_command = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : ""
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def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
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"""
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kraken2 \\
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--db $db \\
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--threads $task.cpus \\
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--unclassified-out $unclassified \\
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--classified-out $classified \\
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--report ${prefix}.kraken2.report.txt \\
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--gzip-compressed \\
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$unclassified_command \\
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$classified_command \\
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$readclassification_command \\
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$paired \\
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$args \\
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$reads
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pigz -p $task.cpus *.fastq
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$compress_reads_command
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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25
modules/nf-core/modules/kraken2/kraken2/meta.yml
generated
25
modules/nf-core/modules/kraken2/kraken2/meta.yml
generated
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@ -27,25 +27,40 @@ input:
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- db:
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type: directory
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description: Kraken2 database
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- save_output_fastqs:
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type: boolean
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description: |
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If true, optional commands are added to save classified and unclassified reads
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as fastq files
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- save_reads_assignment:
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type: boolean
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description: |
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If true, an optional command is added to save a file reporting the taxonomic
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classification of each input read
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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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- classified:
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- classified_reads_fastq:
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type: file
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description: |
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Reads classified to belong to any of the taxa
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Reads classified as belonging to any of the taxa
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on the Kraken2 database.
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pattern: "*{fastq.gz}"
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- unclassified:
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- unclassified_reads_fastq:
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type: file
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description: |
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Reads not classified to belong to any of the taxa
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Reads not classified to any of the taxa
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on the Kraken2 database.
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pattern: "*{fastq.gz}"
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- txt:
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- classified_reads_assignment:
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type: file
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description: |
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Kraken2 output file indicating the taxonomic assignment of
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each input read
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- report:
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type: file
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description: |
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Kraken2 report containing stats about classified
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@ -94,16 +94,17 @@ params {
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// MALT
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run_malt = false
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malt_mode = 'BlastN'
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malt_generatemegansummary = false
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malt_generate_megansummary = false
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malt_save_reads = false
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// kraken2
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run_kraken2 = false
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run_kraken2 = false
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kraken2_save_reads = false
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kraken2_save_readclassification = false
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// centrifuge
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run_centrifuge = false
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centrifuge_save_unaligned = false
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centrifuge_save_aligned = false
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centrifuge_sam_format = false
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centrifuge_save_reads = false
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// metaphlan3
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run_metaphlan3 = false
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@ -114,7 +115,8 @@ params {
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// diamond
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run_diamond = false
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diamond_output_format = 'txt'
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diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently
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diamond_save_reads = false // this will override diamound output format so no taxonomic profile is generated!
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}
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// Load base.config by default for all pipelines
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@ -10,7 +10,10 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": ["input", "outdir"],
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"required": [
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"input",
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"outdir"
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],
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"properties": {
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"input": {
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"type": "string",
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@ -173,7 +176,14 @@
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"description": "Method used to save pipeline results to output directory.",
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"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
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"fa_icon": "fas fa-copy",
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"hidden": true
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},
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"email_on_fail": {
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@ -278,15 +288,6 @@
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"run_centrifuge": {
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"type": "boolean"
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},
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"centrifuge_save_unaligned": {
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"type": "boolean"
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},
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"centrifuge_save_aligned": {
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"type": "boolean"
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},
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"centrifuge_sam_format": {
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"type": "boolean"
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},
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"run_metaphlan3": {
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"type": "boolean",
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"description": "Enable MetaPhlAn for taxonomic profiling"
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@ -294,7 +295,10 @@
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp",
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"enum": ["fastp", "adapterremoval"]
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"enum": [
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"fastp",
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"adapterremoval"
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]
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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@ -335,7 +339,10 @@
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": ["entropy", "dust"]
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"enum": [
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"entropy",
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"dust"
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]
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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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@ -385,13 +392,20 @@
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"run_kaiju": {
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"type": "boolean"
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},
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"malt_generatemegansummary": {
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"malt_generate_megansummary": {
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"type": "boolean"
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},
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"kaiju_taxon_name": {
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"type": "string",
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"default": "species",
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"enum": ["phylum", "class", "order", "family", "genus", "species"]
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"enum": [
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"phylum",
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"class",
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"order",
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"family",
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"genus",
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"species"
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]
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},
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"run_diamond": {
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"type": "boolean"
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@ -399,11 +413,34 @@
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"diamond_output_format": {
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"type": "string",
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"default": "tsv",
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"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
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"enum": [
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"blast",
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"xml",
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"txt",
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"daa",
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"sam",
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"tsv",
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"paf"
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]
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},
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"longread_hostremoval_index": {
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"type": "string",
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"default": "None"
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},
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"malt_save_reads": {
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"type": "boolean"
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},
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"kraken2_save_reads": {
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"type": "boolean"
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},
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"kraken2_save_readclassification": {
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"type": "boolean"
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},
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"centrifuge_save_reads": {
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"type": "boolean"
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},
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"diamond_save_reads": {
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"type": "boolean"
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}
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}
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}
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}
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@ -65,10 +65,18 @@ workflow PROFILING {
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ch_input_for_malt = ch_input_for_profiling.malt
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.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
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.map {
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it ->
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def temp_meta = [ id: it[2]['db_name']] + it[2]
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def db = it[3]
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[ temp_meta, it[1], db ]
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meta, reads, db_meta, db ->
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def sam_format = params.malt_save_reads ? ' --alignments' : ""
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// TODO No MALT SAM?
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// TODO check all aligned reads published
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// TODO try turning on/off aligned reads
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// TODO wut? [9a/a441d6] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MALT_RUN (null)
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def temp_meta = [ id: meta['db_name'] ]
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def new_db_meta = db_meta.clone()
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new_db_meta['db_params'] = db_meta['db_params'] + sam_format
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def new_meta = temp_meta + new_db_meta
|
||||
|
||||
[ new_meta, reads, db ]
|
||||
}
|
||||
.groupTuple(by: [0,2])
|
||||
.multiMap {
|
||||
|
@ -92,7 +100,7 @@ workflow PROFILING {
|
|||
[ meta_new, rma ]
|
||||
}
|
||||
|
||||
MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generatemegansummary )
|
||||
MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generate_megansummary )
|
||||
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
|
||||
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
|
||||
|
@ -108,10 +116,10 @@ workflow PROFILING {
|
|||
db: it[3]
|
||||
}
|
||||
|
||||
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
|
||||
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
|
||||
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
|
||||
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) )
|
||||
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.txt )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
|
||||
|
||||
}
|
||||
|
||||
|
@ -128,7 +136,7 @@ workflow PROFILING {
|
|||
db: it[3]
|
||||
}
|
||||
|
||||
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format )
|
||||
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads )
|
||||
CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
|
||||
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
|
||||
|
@ -180,9 +188,13 @@ workflow PROFILING {
|
|||
db: it[3]
|
||||
}
|
||||
|
||||
DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format )
|
||||
// diamond only accepts single output file specification, therefore
|
||||
// this will replace output file!
|
||||
ch_diamond_reads_format = params.diamond_save_reads ? 'sam' : params.diamond_output_format
|
||||
|
||||
DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format, [] )
|
||||
ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.output )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.tsv )
|
||||
|
||||
}
|
||||
|
||||
|
|
|
@ -29,6 +29,8 @@ if (params.hostremoval_reference ) { ch_reference = file(params.hostre
|
|||
if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = file(params.shortread_hostremoval_index ) } else { ch_shortread_reference_index = [] }
|
||||
if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] }
|
||||
|
||||
if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. Only aligned reads in SAM format will be produced, no taxonomic profiles will be available."
|
||||
|
||||
/*
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
CONFIG FILES
|
||||
|
|
Loading…
Reference in a new issue