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Merge pull request #91 from MillironX/feature/kreport2krona
Add Krona output for Kraken classification
This commit is contained in:
commit
5e554a3a0b
14 changed files with 288 additions and 0 deletions
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@ -36,6 +36,10 @@
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> Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.
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> Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.
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- [Krona](https://doi.org/10.1186/1471-2105-12-385)
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> Ondov, Brian D., Nicholas H. Bergman, and Adam M. Phillippy. 2011. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12 (1): 385. doi: 10.1186/1471-2105-12-385.
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- [MALT](https://doi.org/10.1038/s41559-017-0446-6)
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- [MALT](https://doi.org/10.1038/s41559-017-0446-6)
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> Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico. Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6.
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> Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico. Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6.
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@ -293,6 +293,14 @@ process {
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]
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]
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}
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}
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withName: KRONA_KTIMPORTTEXT {
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publishDir = [
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path: { "${params.outdir}/krona" },
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mode: params.publish_dir_mode,
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pattern: '*.{html}'
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]
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}
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withName: METAPHLAN3 {
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withName: METAPHLAN3 {
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ext.args = { "${meta.db_params}" }
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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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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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@ -37,6 +37,7 @@ params {
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run_metaphlan3 = true
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run_metaphlan3 = true
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run_centrifuge = true
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run_centrifuge = true
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run_diamond = true
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run_diamond = true
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run_krona = true
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malt_save_reads = true
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malt_save_reads = true
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kraken2_save_reads = true
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kraken2_save_reads = true
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centrifuge_save_reads = true
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centrifuge_save_reads = true
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@ -37,6 +37,7 @@ params {
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run_metaphlan3 = true
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run_metaphlan3 = true
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run_centrifuge = true
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run_centrifuge = true
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run_diamond = true
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run_diamond = true
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run_krona = true
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}
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}
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process {
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process {
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@ -48,6 +48,12 @@
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"kraken2/kraken2": {
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"kraken2/kraken2": {
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"git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
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"git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
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},
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},
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"krakentools/kreport2krona": {
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"git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
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},
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"krona/ktimporttext": {
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"git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"
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},
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"malt/run": {
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"malt/run": {
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"git_sha": "be8d7b3293cac26cc63e4dbfb364deb8ed6ec7e5"
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"git_sha": "be8d7b3293cac26cc63e4dbfb364deb8ed6ec7e5"
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},
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},
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40
modules/local/krona_cleanup.nf
Normal file
40
modules/local/krona_cleanup.nf
Normal file
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@ -0,0 +1,40 @@
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process KRONA_CLEANUP {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
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'biocontainers/biocontainers:v1.2.0_cv1' }"
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input:
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tuple val(meta), path(krona, stageAs: 'uncleaned.krona.txt')
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output:
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tuple val(meta), path("*.txt"), emit: txt
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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# Copy the file to a new name
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cp ${krona} ${prefix}.txt
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# Remove ugly 'x__' prefixes for each of the taxonomic levels
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LEVELS=(d k p c o f g s)
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for L in "\${LEVELS[@]}"; do
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sed -i "s/\${L}__//g" ${prefix}.txt
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done
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# Remove underscores that are standing in place of spaces
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sed -i "s/_/ /g" ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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36
modules/nf-core/modules/krakentools/kreport2krona/main.nf
generated
Normal file
36
modules/nf-core/modules/krakentools/kreport2krona/main.nf
generated
Normal file
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@ -0,0 +1,36 @@
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def VERSION = '1.2' // Version information not provided by tool on CLI
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process KRAKENTOOLS_KREPORT2KRONA {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
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'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
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input:
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tuple val(meta), path(kreport)
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output:
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tuple val(meta), path("*.txt"), emit: txt
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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 prefix = task.ext.prefix ?: "${meta.id}"
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"""
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kreport2krona.py \\
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-r ${kreport} \\
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-o ${prefix}.txt \\
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${args}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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kreport2krona.py: ${VERSION}
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END_VERSIONS
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"""
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}
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41
modules/nf-core/modules/krakentools/kreport2krona/meta.yml
generated
Normal file
41
modules/nf-core/modules/krakentools/kreport2krona/meta.yml
generated
Normal file
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@ -0,0 +1,41 @@
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name: krakentools_kreport2krona
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description: Takes a Kraken report file and prints out a krona-compatible TEXT file
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keywords:
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- kraken
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- krona
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- metagenomics
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- visualization
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tools:
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- krakentools:
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description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
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homepage: https://github.com/jenniferlu717/KrakenTools
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licence: ["GPL v3"]
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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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- kreport:
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type: file
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description: Kraken report
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pattern: "*.{txt,kreport}"
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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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- 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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- krona:
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type: file
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description: Krona text-based input file converted from Kraken report
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pattern: "*.{txt,krona}"
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authors:
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- "@MillironX"
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34
modules/nf-core/modules/krona/ktimporttext/main.nf
generated
Normal file
34
modules/nf-core/modules/krona/ktimporttext/main.nf
generated
Normal file
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@ -0,0 +1,34 @@
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process KRONA_KTIMPORTTEXT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::krona=2.8.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
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'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
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input:
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tuple val(meta), path(report)
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output:
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tuple val(meta), path ('*.html'), emit: html
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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ktImportText \\
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$args \\
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-o ${prefix}.html \\
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$report
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g')
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END_VERSIONS
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"""
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}
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47
modules/nf-core/modules/krona/ktimporttext/meta.yml
generated
Normal file
47
modules/nf-core/modules/krona/ktimporttext/meta.yml
generated
Normal file
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@ -0,0 +1,47 @@
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name: "krona_ktimporttext"
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description: Creates a Krona chart from text files listing quantities and lineages.
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keywords:
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- plot
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- taxonomy
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- interactive
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- html
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- visualisation
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- krona chart
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- metagenomics
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tools:
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- krona:
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description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
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homepage: https://github.com/marbl/Krona/wiki/KronaTools
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documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
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tool_dev_url: https://github.com/marbl/Krona
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doi: 10.1186/1471-2105-12-385
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licence: https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt
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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']
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- report:
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type: file
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description: "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored."
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pattern: "*.{txt}"
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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' ]
|
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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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- html:
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type: file
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description: A html file containing an interactive krona plot.
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pattern: "*.{html}"
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|
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|
authors:
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|
- "@jianhong"
|
|
@ -125,6 +125,9 @@ params {
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run_diamond = false
|
run_diamond = false
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diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently
|
diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently
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diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated!
|
diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated!
|
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|
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|
// krona
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|
run_krona = false
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}
|
}
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|
|
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// Load base.config by default for all pipelines
|
// Load base.config by default for all pipelines
|
||||||
|
|
|
@ -433,6 +433,9 @@
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},
|
},
|
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"diamond_save_reads": {
|
"diamond_save_reads": {
|
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"type": "boolean"
|
"type": "boolean"
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|
},
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|
"run_krona": {
|
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|
"type": "boolean"
|
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}
|
}
|
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}
|
}
|
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}
|
}
|
||||||
|
|
55
subworkflows/local/visualization_krona.nf
Normal file
55
subworkflows/local/visualization_krona.nf
Normal file
|
@ -0,0 +1,55 @@
|
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|
//
|
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|
// Create Krona visualizations
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|
//
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|
|
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|
include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
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include { KRONA_CLEANUP } from '../../modules/local/krona_cleanup'
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include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/modules/krona/ktimporttext/main'
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|
|
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|
workflow VISUALIZATION_KRONA {
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|
take:
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|
profiles
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|
|
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|
main:
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|
ch_krona_text = Channel.empty()
|
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|
ch_krona_html = Channel.empty()
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|
ch_versions = Channel.empty()
|
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|
|
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|
/*
|
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|
Split profile results based on tool they come from
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|
*/
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|
ch_input_profiles = profiles
|
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|
.branch {
|
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|
kraken2: it[0]['tool'] == 'kraken2'
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|
unknown: true
|
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|
}
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|
|
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|
/*
|
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|
Convert Kraken2 formatted reports into Krona text files
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||||||
|
*/
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|
ch_kraken_reports = ch_input_profiles.kraken2
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||||||
|
KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports )
|
||||||
|
ch_krona_text = ch_krona_text.mix( KRAKENTOOLS_KREPORT2KRONA.out.txt )
|
||||||
|
ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
|
||||||
|
|
||||||
|
/*
|
||||||
|
Remove taxonomy level annotations from the Krona text files
|
||||||
|
*/
|
||||||
|
KRONA_CLEANUP( ch_krona_text )
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||||||
|
ch_cleaned_krona_text = KRONA_CLEANUP.out.txt
|
||||||
|
ch_versions = ch_versions.mix( KRONA_CLEANUP.out.versions.first() )
|
||||||
|
|
||||||
|
/*
|
||||||
|
Convert Krona text files into html Krona visualizations
|
||||||
|
*/
|
||||||
|
ch_krona_text_for_import = ch_cleaned_krona_text
|
||||||
|
.map{[[id: it[0]['db_name']], it[1]]}
|
||||||
|
.groupTuple()
|
||||||
|
KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
|
||||||
|
ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
|
||||||
|
ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
|
||||||
|
|
||||||
|
emit:
|
||||||
|
html = ch_krona_html
|
||||||
|
versions = ch_versions
|
||||||
|
}
|
|
@ -62,6 +62,7 @@ include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_
|
||||||
include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_hostremoval'
|
include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_hostremoval'
|
||||||
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
|
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
|
||||||
include { PROFILING } from '../subworkflows/local/profiling'
|
include { PROFILING } from '../subworkflows/local/profiling'
|
||||||
|
include { VISUALIZATION_KRONA } from '../subworkflows/local/visualization_krona'
|
||||||
|
|
||||||
/*
|
/*
|
||||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||||
|
@ -209,6 +210,14 @@ workflow TAXPROFILER {
|
||||||
PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
|
PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
|
||||||
ch_versions = ch_versions.mix( PROFILING.out.versions )
|
ch_versions = ch_versions.mix( PROFILING.out.versions )
|
||||||
|
|
||||||
|
/*
|
||||||
|
SUBWORKFLOW: VISUALIZATION_KRONA
|
||||||
|
*/
|
||||||
|
if ( params.run_krona ) {
|
||||||
|
VISUALIZATION_KRONA ( PROFILING.out.profiles )
|
||||||
|
ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
|
||||||
|
}
|
||||||
|
|
||||||
/*
|
/*
|
||||||
MODULE: MultiQC
|
MODULE: MultiQC
|
||||||
*/
|
*/
|
||||||
|
|
Loading…
Reference in a new issue