mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:23:09 +00:00
Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file
This commit is contained in:
parent
27f174d17e
commit
02c06b9f7b
8 changed files with 206 additions and 3 deletions
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@ -273,7 +273,7 @@ process {
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]
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]
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}
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}
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withName: MEGAN_RMA2INFO {
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withName: 'NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO' {
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ext.args = "-c2c Taxonomy"
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ext.args = "-c2c Taxonomy"
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ext.prefix = { "${meta.id}" }
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ext.prefix = { "${meta.id}" }
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publishDir = [
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publishDir = [
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@ -293,7 +293,32 @@ process {
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]
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]
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}
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}
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withName: KRONA_CLEANUP {
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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}/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: KRONA_KTIMPORTTEXT {
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withName: KRONA_KTIMPORTTEXT {
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ext.prefix = { "${meta.tool}-${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/krona" },
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mode: params.publish_dir_mode,
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pattern: '*.{html}'
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]
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}
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withName: 'NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO' {
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ext.args = { "--read2class Taxonomy" }
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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}
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withName: KRONA_KTIMPORTTAXONOMY {
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ext.args = "-i"
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ext.prefix = { "${meta.tool}-${meta.id}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/krona" },
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path: { "${params.outdir}/krona" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -39,6 +39,9 @@
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"filtlong": {
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"filtlong": {
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"git_sha": "089f761f0bf79c4a486f1df9b6205f650196a2c1"
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"git_sha": "089f761f0bf79c4a486f1df9b6205f650196a2c1"
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},
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},
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"gunzip": {
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"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
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},
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"kaiju/kaiju": {
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"kaiju/kaiju": {
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"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
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"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
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},
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},
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@ -54,6 +57,9 @@
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"krakentools/kreport2krona": {
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"krakentools/kreport2krona": {
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"git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
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"git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
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},
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},
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"krona/ktimporttaxonomy": {
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"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
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},
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"krona/ktimporttext": {
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"krona/ktimporttext": {
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"git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"
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"git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"
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},
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},
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34
modules/nf-core/modules/gunzip/main.nf
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34
modules/nf-core/modules/gunzip/main.nf
generated
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@ -0,0 +1,34 @@
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process GUNZIP {
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tag "$archive"
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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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
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'ubuntu:20.04' }"
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input:
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tuple val(meta), path(archive)
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output:
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tuple val(meta), path("$gunzip"), emit: gunzip
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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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gunzip = archive.toString() - '.gz'
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"""
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gunzip \\
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-f \\
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$args \\
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$archive
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
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END_VERSIONS
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"""
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}
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34
modules/nf-core/modules/gunzip/meta.yml
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34
modules/nf-core/modules/gunzip/meta.yml
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@ -0,0 +1,34 @@
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name: gunzip
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description: Compresses and decompresses files.
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keywords:
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- gunzip
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- compression
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tools:
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- gunzip:
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description: |
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gzip is a file format and a software application used for file compression and decompression.
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documentation: https://www.gnu.org/software/gzip/manual/gzip.html
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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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Optional groovy Map containing meta information
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e.g. [ id:'test', single_end:false ]
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- archive:
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type: file
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description: File to be compressed/uncompressed
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pattern: "*.*"
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output:
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- gunzip:
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type: file
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description: Compressed/uncompressed file
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pattern: "*.*"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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- "@jfy133"
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38
modules/nf-core/modules/krona/ktimporttaxonomy/main.nf
generated
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38
modules/nf-core/modules/krona/ktimporttaxonomy/main.nf
generated
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@ -0,0 +1,38 @@
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process KRONA_KTIMPORTTAXONOMY {
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tag "${meta.id}"
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label 'process_high'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::krona=2.8" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' :
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'quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2' }"
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input:
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tuple val(meta), path(report)
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path taxonomy
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output:
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tuple val(meta), path ('*.html'), emit: html
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = '2.8' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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ktImportTaxonomy \\
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$args \\
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-o ${prefix}.html \\
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-tax $taxonomy \\
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$report
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krona: $VERSION
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END_VERSIONS
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"""
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}
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47
modules/nf-core/modules/krona/ktimporttaxonomy/meta.yml
generated
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47
modules/nf-core/modules/krona/ktimporttaxonomy/meta.yml
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@ -0,0 +1,47 @@
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name: krona_ktimporttaxonomy
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description: KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot.
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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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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:
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doi: https://doi.org/10.1186/1471-2105-12-385
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licence:
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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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- database:
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type: file
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description: |
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Path to the taxonomy database .tab file downloaded by krona/ktUpdateTaxonomy
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The file will be saved under a folder named "taxonomy" as "taxonomy/taxonomy.tab".
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The parent folder will be passed as argument to ktImportTaxonomy.
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- report:
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type: file
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description: "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored."
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pattern: "*.{tsv}"
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output:
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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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authors:
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- "@mjakobs"
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@ -2,10 +2,13 @@
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// Create Krona visualizations
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// Create Krona visualizations
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//
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//
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include { MEGAN_RMA2INFO } from '../../modules/nf-core/modules/megan/rma2info/main'
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include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/modules/kaiju/kaiju2krona/main'
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include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/modules/kaiju/kaiju2krona/main'
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include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
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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_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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include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/modules/krona/ktimporttext/main'
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include { KRONA_KTIMPORTTAXONOMY } from '../../modules/nf-core/modules/krona/ktimporttaxonomy/main'
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include { GUNZIP } from '../../modules/nf-core/modules/gunzip/main'
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workflow VISUALIZATION_KRONA {
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workflow VISUALIZATION_KRONA {
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take:
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take:
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@ -30,6 +33,7 @@ workflow VISUALIZATION_KRONA {
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ch_input_classifications = classifications
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ch_input_classifications = classifications
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.branch {
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.branch {
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kaiju: it[0]['tool'] == 'kaiju'
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kaiju: it[0]['tool'] == 'kaiju'
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malt: it[0]['tool'] == 'malt'
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unknown: true
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unknown: true
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}
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}
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Convert Krona text files into html Krona visualizations
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Convert Krona text files into html Krona visualizations
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*/
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*/
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ch_krona_text_for_import = ch_cleaned_krona_text
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ch_krona_text_for_import = ch_cleaned_krona_text
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.map{[[id: it[0]['db_name']], it[1]]}
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.map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
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.groupTuple()
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.groupTuple()
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.dump(tag: "text")
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KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
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KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
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ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
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ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
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ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
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ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
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/*
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/*
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Convert Krona
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Convert MALT/MEGAN RMA2INFO files into html Krona visualisations
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*/
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*/
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if ( params.krona_taxonomy_directory ) {
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MEGAN_RMA2INFO ( ch_input_classifications.malt, false )
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GUNZIP ( MEGAN_RMA2INFO.out.txt )
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ch_krona_taxonomy_for_input = GUNZIP.out.gunzip
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.map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
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.groupTuple()
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.dump(tag: "taxonomy")
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KRONA_KTIMPORTTAXONOMY ( ch_krona_taxonomy_for_input, file(params.krona_taxonomy_directory, checkExists: true) )
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ch_krona_html.mix( KRONA_KTIMPORTTAXONOMY.out.html )
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ch_versions = ch_versions.mix( MEGAN_RMA2INFO.out.versions.first() )
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ch_versions = ch_versions.mix( KRONA_KTIMPORTTAXONOMY.out.versions.first() )
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}
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emit:
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emit:
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html = ch_krona_html
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html = ch_krona_html
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if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. As --diamond_save_reads supplied, only aligned reads in SAM format will be produced, no taxonomic profiles will be available."
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if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. As --diamond_save_reads supplied, only aligned reads in SAM format will be produced, no taxonomic profiles will be available."
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if (params.run_malt && params.run_krona && !params.krona_taxonomy_directory) log.warn "[nf-core/taxprofiler] Krona can only be run on MALT output if path to Krona taxonomy database supplied to --krona_taxonomy_directory. Krona will not be executed in this run for MALT."
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/*
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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CONFIG FILES
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CONFIG FILES
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