From cdefbec66999c0b49d8bfeea9d6f9d19056635a2 Mon Sep 17 00:00:00 2001 From: JIANHONG OU Date: Thu, 28 Apr 2022 08:16:26 -0400 Subject: [PATCH] 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 * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates * 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 --- modules/krona/ktimporttext/main.nf | 34 ++++++++++++++ modules/krona/ktimporttext/meta.yml | 47 +++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/config/test_data.config | 3 ++ tests/modules/krona/ktimporttext/main.nf | 31 ++++++++++++ .../krona/ktimporttext/nextflow.config | 5 ++ tests/modules/krona/ktimporttext/test.yml | 19 ++++++++ 7 files changed, 143 insertions(+) create mode 100644 modules/krona/ktimporttext/main.nf create mode 100644 modules/krona/ktimporttext/meta.yml create mode 100644 tests/modules/krona/ktimporttext/main.nf create mode 100644 tests/modules/krona/ktimporttext/nextflow.config create mode 100644 tests/modules/krona/ktimporttext/test.yml diff --git a/modules/krona/ktimporttext/main.nf b/modules/krona/ktimporttext/main.nf new file mode 100644 index 00000000..de0cfc22 --- /dev/null +++ b/modules/krona/ktimporttext/main.nf @@ -0,0 +1,34 @@ +process KRONA_KTIMPORTTEXT { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1': + 'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }" + + input: + tuple val(meta), path(report) + + output: + tuple val(meta), path ('*.html'), emit: html + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + ktImportText \\ + $args \\ + -o ${prefix}.html \\ + $report + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g') + END_VERSIONS + """ +} diff --git a/modules/krona/ktimporttext/meta.yml b/modules/krona/ktimporttext/meta.yml new file mode 100644 index 00000000..a7108e0d --- /dev/null +++ b/modules/krona/ktimporttext/meta.yml @@ -0,0 +1,47 @@ +name: "krona_ktimporttext" +description: Creates a Krona chart from text files listing quantities and lineages. +keywords: + - plot + - taxonomy + - interactive + - html + - visualisation + - krona chart + - metagenomics +tools: + - krona: + description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. + homepage: https://github.com/marbl/Krona/wiki/KronaTools + documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html + tool_dev_url: https://github.com/marbl/Krona + doi: 10.1186/1471-2105-12-385 + licence: https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - report: + type: file + 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." + pattern: "*.{txt}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - html: + type: file + description: A html file containing an interactive krona plot. + pattern: "*.{html}" + +authors: + - "@jianhong" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 4d8ce0b5..dfcbfa8c 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1050,6 +1050,10 @@ krona/ktimporttaxonomy: - modules/krona/ktimporttaxonomy/** - tests/modules/krona/ktimporttaxonomy/** +krona/ktimporttext: + - modules/krona/ktimporttext/** + - tests/modules/krona/ktimporttext/** + last/dotplot: - modules/last/dotplot/** - tests/modules/last/dotplot/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config index b3171a51..5d5535c4 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -109,6 +109,9 @@ params { test_sequencing_summary = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt" } + 'metagenome' { + kraken_report = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.report.txt" + } } 'homo_sapiens' { 'genome' { diff --git a/tests/modules/krona/ktimporttext/main.nf b/tests/modules/krona/ktimporttext/main.nf new file mode 100644 index 00000000..3d288b7b --- /dev/null +++ b/tests/modules/krona/ktimporttext/main.nf @@ -0,0 +1,31 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { KRONA_KTIMPORTTEXT } from '../../../../modules/krona/ktimporttext/main.nf' + +workflow test_krona_ktimporttext_multi { + + input = [ + [ id:'test', single_end:false ], // meta map + [ + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/ktimporttext.txt', checkIfExists: true), // krona default test file + file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true), //Kraken2 report file + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/kaiju_out4krona.txt', checkIfExists: true) // Kaiju output 4 krona + ] + ] + + KRONA_KTIMPORTTEXT ( input ) +} + +workflow test_krona_ktimporttext_single { + + input = [ + [ id:'test', single_end:false ], // meta map + [ + file('http://krona.sourceforge.net/examples/text.txt', checkIfExists: true) // krona default test file + ] + ] + + KRONA_KTIMPORTTEXT ( input ) +} diff --git a/tests/modules/krona/ktimporttext/nextflow.config b/tests/modules/krona/ktimporttext/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/krona/ktimporttext/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/krona/ktimporttext/test.yml b/tests/modules/krona/ktimporttext/test.yml new file mode 100644 index 00000000..93ae12da --- /dev/null +++ b/tests/modules/krona/ktimporttext/test.yml @@ -0,0 +1,19 @@ +- name: krona ktimporttext test_krona_ktimporttext_multi + command: nextflow run tests/modules/krona/ktimporttext -entry test_krona_ktimporttext_multi -c tests/config/nextflow.config + tags: + - krona + - krona/ktimporttext + files: + - path: output/krona/test.html + contains: + - "DOCTYPE html PUBLIC" + +- name: krona ktimporttext test_krona_ktimporttext_single + command: nextflow run tests/modules/krona/ktimporttext -entry test_krona_ktimporttext_single -c tests/config/nextflow.config + tags: + - krona + - krona/ktimporttext + files: + - path: output/krona/test.html + contains: + - "DOCTYPE html PUBLIC"