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Update the tests for MultiQC

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This commit is contained in:
Abhinav Sharma 2020-12-02 12:38:41 +05:30
parent 4e657c82e2
commit 5fd3ba3ce6
4 changed files with 23 additions and 21 deletions
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9
.github/workflows/multiqc.yml vendored
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@ -26,5 +26,12 @@ jobs:
wget -qO- get.nextflow.io | bash wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module # Test the module
- run: nextflow run ./software/multiqc/test/ -profile docker - run: pytest --tag multiqc --symlink --wt 2

22
software/multiqc/main.nf
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@ -2,31 +2,29 @@
include { initOptions; saveFiles; getSoftwareName } from './functions' include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:] params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
process MULTIQC { process MULTIQC {
tag "multiqc" tag "multiqc"
label 'process_medium' label 'process_medium'
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda(params.enable_conda ? "bioconda::multiqc=1.9" : null) conda (params.enable_conda ? "bioconda::multiqc=1.9" : null)
container "quay.io/biocontainers/multiqc:1.9--py_1" container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
input: input:
path(generic_report) tuple val(meta), path(reads)
output: output:
path "multiqc_data", emit: dir path "*multiqc_report.html", emit: report
path "multiqc_report.html", emit: html path "*_data" , emit: data
path "*.version.txt", emit: version path "*_plots" , optional:true, emit: plots
script: script:
def software = getSoftwareName(task.process)
""" """
multiqc . multiqc -f $options.args .
multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
""" """
} }

8
tests/software/multiqc/main.nf
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@ -10,10 +10,10 @@ workflow test_multiqc {
def input = [] def input = []
input = [[id: 'test'], // meta map input = [[id: 'test'], // meta map
[file("${launchDir}/tests/data/fastqc/test_1.fastq.html", checkIfExists: true), [file("${launchDir}/tests/data/fastqc/test_1_fastqc.html", checkIfExists: true),
file("${launchDir}/tests/data/fastqc/test_1.fastq.zip", checkIfExists: true), file("${launchDir}/tests/data/fastqc/test_1_fastqc.zip", checkIfExists: true),
file("${launchDir}/tests/data/fastqc/test_2.fastq.html", checkIfExists: true), file("${launchDir}/tests/data/fastqc/test_2_fastqc.html", checkIfExists: true),
file("${launchDir}/tests/data/fastqc/test_2.fastq.zip", checkIfExists: true)]] file("${launchDir}/tests/data/fastqc/test_2_fastqc.zip", checkIfExists: true)]]
MULTIQC(input) MULTIQC(input)
} }

5
tests/software/multiqc/test.yml
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@ -3,7 +3,4 @@
tags: tags:
- multiqc - multiqc
files: files:
- path: output/test_multiqc/test_fastqc.html - path: output/test_multiqc/multiqc_report.html
md5sum: 7027e72c3e55292c1567f12e02565e3b
- path: output/test_multiqc/test_fastqc.html
md5sum: 7027e72c3e55292c1567f12e02565e3b