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new module: datavzrd (#5883)
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* Generated structure for new module

* Implemented module

* Added semi-functional tests

* Cleaned tests - test don't work yet

* fix main, start nf-test

* add new test data

* fix linting

* try to assert folders

* fix tests

* change output to prefix

* change to prefix

* update to prefix

---------

Co-authored-by: vickylaram <mielczarekv@rki.de>
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@famosab @vickylaram
famosab and vickylaram authored Jun 26, 2024
1 parent 373d3e2 commit 320e735
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7 changes: 7 additions & 0 deletions modules/nf-core/datavzrd/environment.yml
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name: datavzrd
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- conda-forge::datavzrd==2.36.12
63 changes: 63 additions & 0 deletions modules/nf-core/datavzrd/main.nf
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process DATAVZRD {
tag "$meta.id"
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://community.wave.seqera.io/library/datavzrd:2.36.12--bb93c8c988b7a9af':
'community.wave.seqera.io/library/datavzrd:2.36.12--593eb75e566b7f2a' }"

input:
tuple val(meta), file(config_file), file(table)

output:
tuple val(meta), path("${prefix}"), emit: report
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir ${prefix}
datavzrd \\
${args} \\
${config_file} \\
--output ${prefix} \\
cat <<-END_VERSIONS > versions.yml
"${task.process}":
datavzrd: \$(echo \$( datavzrd --version | sed -e 's/[^0-9.]//g' ))
END_VERSIONS
"""

stub:
prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir ${prefix}
mkdir ${prefix}/static
mkdir ${prefix}/network
mkdir ${prefix}/network/data
mkdir ${prefix}/network/plots
touch ./${prefix}/index.html
touch ./${prefix}/static/bootstrap.min.css
touch ./${prefix}/static/bootstrap-select.min.css
touch ./${prefix}/static/bootstrap-table.min.css
touch ./${prefix}/static/bootstrap-table-fixed-columns.min.css
touch ./${prefix}/static/bundle.js
touch ./${prefix}/static/datavzrd.css
touch ./${prefix}/network/index_1.html
touch ./${prefix}/network/config.js
touch ./${prefix}/network/functions.js
touch ./${prefix}/network/heatmap.js
touch ./${prefix}/network/data/data_1.js
touch ./${prefix}/network/plots/plot_0.js
cat <<-END_VERSIONS > versions.yml
"${task.process}":
datavzrd: \$(echo \$( datavzrd --version | sed -e 's/[^0-9.]//g' ))
END_VERSIONS
"""
}
46 changes: 46 additions & 0 deletions modules/nf-core/datavzrd/meta.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "datavzrd"
description: Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.
keywords:
- visualisation
- tsv
- csv
tools:
- datavzrd:
description: Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.
homepage: https://datavzrd.github.io/
documentation: https://datavzrd.github.io/docs/index.html
tool_dev_url: https://github.com/datavzrd/datavzrd
licence: ["MIT"]

input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- config_file:
type: file
description: configuration file used for visualisation
pattern: "*.{yml,yaml}"
- table:
type: file
description: file used for visualisation
pattern: "*.{tsv,csv}"

output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- report:
type: directory
description: directory with HTML report of provided CSV/TSV files
pattern: "/output/"

authors:
- "@vickylaram"
- "@famosab"
maintainers:
- "@famosab"
112 changes: 112 additions & 0 deletions modules/nf-core/datavzrd/tests/main.nf.test
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nextflow_process {
name "Test Process DATAVZRD"
script "../main.nf"
process "DATAVZRD"
tag "modules"
tag "modules_nfcore"
tag "datavzrd"

test("csv") {

when {
process {
"""
input[0] = [ [id: "csv_config"],
file(params.modules_testdata_base_path + 'generic/config/config_test.datavzrd.yaml', checkIfExists: true),
file(params.modules_testdata_base_path + 'generic/csv/test.csv', checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
path(process.out.report[0][1])
.list()
.collect { getRecursiveFileNames(it, process.out.report[0][1]) }
.flatten()
).match("csv")
}
)
}
}

test("tsv") {

when {
process {
"""
input[0] = [ [id: "tsv_config"],
file(params.modules_testdata_base_path + 'generic/config/config_network.datavzrd.yaml', checkIfExists: true),
file(params.modules_testdata_base_path + 'generic/tsv/network.tsv', checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
path(process.out.report[0][1])
.list()
.collect { getRecursiveFileNames(it, process.out.report[0][1]) }
.flatten()
).match("tsv")
}
)
}
}

test("csv - stub") {

options "-stub"

when {
process {
"""
input[0] = [ [id: "csv_config"],
file(params.modules_testdata_base_path + 'generic/config/config_test.datavzrd.yaml', checkIfExists: true),
file(params.modules_testdata_base_path + 'generic/csv/test.csv', checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

test("no_config_file") {
when {
process {
"""
input[0] = []
"""
}
}

then {
assertAll(
{ assert process.failed },
{ assert process.out['report'].isEmpty() },
{ assert snapshot(process.out).match() }
)
}
}
}

def getRecursiveFileNames(fileOrDir, outputDir) {
if(file(fileOrDir.toString()).isDirectory()) {
return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
}
return fileOrDir.toString().replace("${outputDir}/", "")
}
162 changes: 162 additions & 0 deletions modules/nf-core/datavzrd/tests/main.nf.test.snap
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{
"csv - stub": {
"content": [
{
"0": [
[
{
"id": "csv_config"
},
[
"index.html:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"config.js:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"data_1.js:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"functions.js:md5,d41d8cd98f00b204e9800998ecf8427e",
"heatmap.js:md5,d41d8cd98f00b204e9800998ecf8427e",
"index_1.html:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"plot_0.js:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
"bootstrap-select.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
"bootstrap-table-fixed-columns.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
"bootstrap-table.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
"bootstrap.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
"bundle.js:md5,d41d8cd98f00b204e9800998ecf8427e",
"datavzrd.css:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
]
],
"1": [
"versions.yml:md5,4c539593d78c0a07ede5759e0ce5ade8"
],
"report": [
[
{
"id": "csv_config"
},
[
"index.html:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"config.js:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"data_1.js:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"functions.js:md5,d41d8cd98f00b204e9800998ecf8427e",
"heatmap.js:md5,d41d8cd98f00b204e9800998ecf8427e",
"index_1.html:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"plot_0.js:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
"bootstrap-select.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
"bootstrap-table-fixed-columns.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
"bootstrap-table.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
"bootstrap.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
"bundle.js:md5,d41d8cd98f00b204e9800998ecf8427e",
"datavzrd.css:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
]
],
"versions": [
"versions.yml:md5,4c539593d78c0a07ede5759e0ce5ade8"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-06-26T10:16:55.267548327"
},
"tsv": {
"content": [
[
"versions.yml:md5,4c539593d78c0a07ede5759e0ce5ade8"
],
[
"index.html",
"network/config.js",
"network/data/data_1.js",
"network/functions.js",
"network/heatmap.js",
"network/index_1.html",
"network/plots/plot_0.js",
"network/plots/plot_1.js",
"network/plots/plot_2.js",
"network/plots/plot_3.js",
"static/bootstrap-select.min.css",
"static/bootstrap-table-fixed-columns.min.css",
"static/bootstrap-table.min.css",
"static/bootstrap.min.css",
"static/bundle.js",
"static/datavzrd.css"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-06-26T10:15:02.495557702"
},
"no_config_file": {
"content": [
{
"0": [

],
"1": [

],
"report": [

],
"versions": [

]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-06-26T10:15:09.362847938"
},
"csv": {
"content": [
[
"versions.yml:md5,4c539593d78c0a07ede5759e0ce5ade8"
],
[
"index.html",
"static/bootstrap-select.min.css",
"static/bootstrap-table-fixed-columns.min.css",
"static/bootstrap-table.min.css",
"static/bootstrap.min.css",
"static/bundle.js",
"static/datavzrd.css",
"test/config.js",
"test/data/data_1.js",
"test/functions.js",
"test/heatmap.js",
"test/index_1.html",
"test/plots/plot_0.js",
"test/plots/plot_1.js",
"test/plots/plot_2.js",
"test/plots/plot_3.js"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-06-26T10:14:58.495338891"
}
}
2 changes: 2 additions & 0 deletions modules/nf-core/datavzrd/tests/tags.yml
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datavzrd:
- "modules/nf-core/datavzrd/**"
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