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add kimporttext module (#1560)
* add kimporttext module * fix the Prettier error. * fix the Prettier error. * fix the test.yml * fix the test.yml * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update the test files; simplify the main script of krona/ktimporttext. * update the test file url for krona ktimporttext Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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34
modules/krona/ktimporttext/main.nf
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34
modules/krona/ktimporttext/main.nf
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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/krona/ktimporttext/meta.yml
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modules/krona/ktimporttext/meta.yml
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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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authors:
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- "@jianhong"
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@ -1050,6 +1050,10 @@ krona/ktimporttaxonomy:
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- modules/krona/ktimporttaxonomy/**
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- tests/modules/krona/ktimporttaxonomy/**
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krona/ktimporttext:
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- modules/krona/ktimporttext/**
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- tests/modules/krona/ktimporttext/**
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last/dotplot:
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- modules/last/dotplot/**
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- tests/modules/last/dotplot/**
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@ -109,6 +109,9 @@ params {
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test_sequencing_summary = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
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}
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'metagenome' {
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kraken_report = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.report.txt"
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}
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}
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'homo_sapiens' {
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'genome' {
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31
tests/modules/krona/ktimporttext/main.nf
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31
tests/modules/krona/ktimporttext/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { KRONA_KTIMPORTTEXT } from '../../../../modules/krona/ktimporttext/main.nf'
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workflow test_krona_ktimporttext_multi {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/ktimporttext.txt', checkIfExists: true), // krona default test file
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file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true), //Kraken2 report file
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file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/kaiju_out4krona.txt', checkIfExists: true) // Kaiju output 4 krona
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]
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]
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KRONA_KTIMPORTTEXT ( input )
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}
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workflow test_krona_ktimporttext_single {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file('http://krona.sourceforge.net/examples/text.txt', checkIfExists: true) // krona default test file
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]
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]
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KRONA_KTIMPORTTEXT ( input )
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}
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5
tests/modules/krona/ktimporttext/nextflow.config
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5
tests/modules/krona/ktimporttext/nextflow.config
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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19
tests/modules/krona/ktimporttext/test.yml
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tests/modules/krona/ktimporttext/test.yml
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- name: krona ktimporttext test_krona_ktimporttext_multi
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command: nextflow run tests/modules/krona/ktimporttext -entry test_krona_ktimporttext_multi -c tests/config/nextflow.config
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tags:
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- krona
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- krona/ktimporttext
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files:
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- path: output/krona/test.html
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contains:
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- "DOCTYPE html PUBLIC"
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- name: krona ktimporttext test_krona_ktimporttext_single
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command: nextflow run tests/modules/krona/ktimporttext -entry test_krona_ktimporttext_single -c tests/config/nextflow.config
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tags:
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- krona
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- krona/ktimporttext
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files:
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- path: output/krona/test.html
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contains:
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- "DOCTYPE html PUBLIC"
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