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Merge pull request #8 from CaroAMN/dev
new module and subworkflow test
2 parents 971a211 + 6e93cc7 commit 2af8f46

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‎conf/test.config‎

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@@ -21,10 +21,7 @@ process {
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset to check pipeline function'
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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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// Define the input data
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input = 'https://raw.githubusercontent.com/CaroAMN/test-datasets/lsmquant/test_data/samplesheets/sample_sheet.csv'
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stage = 'full'
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}

‎modules/local/mat2json/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- "YOUR-TOOL-HERE"

‎modules/local/mat2json/main.nf‎

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process MAT2JSON {
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tag "$meta.id"
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label 'process_single'
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container 'carolinschwitalla/mat2json:latest'
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input:
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tuple val(meta), path(matfile)
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output:
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tuple val(meta), path("*.*"), emit: converted_file
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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/usr/bin/mlrtapp/mat2json $matfile
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mat2json: 1.0
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END_VERSIONS
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"""
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stub:
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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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touch ${prefix}.json
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mat2json: 1.0
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END_VERSIONS
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"""
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}

‎modules/local/mat2json/meta.yml‎

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---
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name: "mat2json"
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description: converst matlab .mat files into json or csv files.
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keywords:
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- file conversion
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- matlab
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- json
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- csv
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tools:
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- "mat2json":
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description: "converst matlab .mat files into json or csv files."
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homepage: ""
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documentation: ""
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tool_dev_url: ""
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doi: ""
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licence:
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identifier:
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input:
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# Only when we have meta
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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:'sample1']`
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- mat_file:
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type: file
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description: matlab file
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pattern: "*.{mat}"
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output:
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- converted_file:
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#Only when we have meta
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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:'sample1', single_end:false ]`
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- "*_conv.*":
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type: file
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description: JSON or CSV file containing the the data from the input .mat file
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pattern: "*.{json,csv}"
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- versions:
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- "versions.yml":
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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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- "@CaroAMN"
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maintainers:
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- "@CaroAMN"

‎modules/local/mat2json/tests/main.nf.test‎

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nextflow_process {
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name "Test Process MAT2JSON"
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script "../main.nf"
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process "MAT2JSON"
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tag "modules"
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tag "modules_"
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tag "mat2json"
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test("matlab file conversion to json") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test'], // meta map
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file('/mnt/ssd/numorph_testdata_s/module_testrun/output_nextflow/intensity/results/variables/thresholds.mat', checkIfExists: true),
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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test("matlab file conversion to json - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id:'test'], // meta map
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file('/mnt/ssd/numorph_testdata_s/module_testrun/output_nextflow/intensity/results/variables/thresholds.mat', checkIfExists: true),
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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}

‎modules/local/mat2json/tests/main.nf.test.snap‎

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{
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"matlab file conversion to json": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test"
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},
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[
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"thresholds.json:md5,88adeb36bb657798c80085b6a58ac58b",
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"versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
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]
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]
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],
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"1": [
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"versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
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],
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"converted_file": [
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[
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{
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"id": "test"
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},
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[
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"thresholds.json:md5,88adeb36bb657798c80085b6a58ac58b",
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"versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
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]
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]
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],
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"versions": [
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"versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.4"
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},
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"timestamp": "2025-02-21T15:36:22.030027548"
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},
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"matlab file conversion to json - stub": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test"
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},
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[
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"test.json:md5,d41d8cd98f00b204e9800998ecf8427e",
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"versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
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]
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]
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],
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"1": [
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"versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
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],
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"converted_file": [
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[
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{
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"id": "test"
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},
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[
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"test.json:md5,d41d8cd98f00b204e9800998ecf8427e",
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"versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
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]
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]
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],
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"versions": [
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"versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.4"
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},
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"timestamp": "2025-02-21T15:36:26.450520824"
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}
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}

subworkflows/local/numorph_preprocessing.nf renamed to subworkflows/local/numorph_preprocessing/main.nf

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@@ -1,9 +1,7 @@
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2-
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include { NUMORPHINTENSITY } from '../../modules/local/numorphintensity/'
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include { NUMORPHALIGN } from '../../modules/local/numorphalign/'
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include { NUMORPHSTITCH } from '../../modules/local/numorphstitch/'
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include { NUMORPHINTENSITY } from '../../../modules/local/numorphintensity/'
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include { NUMORPHALIGN } from '../../../modules/local/numorphalign/'
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include { NUMORPHSTITCH } from '../../../modules/local/numorphstitch/'
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workflow NUMORPH_PREPROCESSING {
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‎subworkflows/local/numorph_preprocessing/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
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name: "numorph_preprocessing"
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## TODO nf-core: Add a description of the subworkflow and list keywords
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description: Sort SAM/BAM/CRAM file
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keywords:
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- sort
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- bam
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- sam
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- cram
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## TODO nf-core: Add a list of the modules and/or subworkflows used in the subworkflow
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components:
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- samtools/sort
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- samtools/index
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## TODO nf-core: List all of the channels used as input with a description and their structure
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input:
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- ch_bam:
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type: file
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description: |
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The input channel containing the BAM/CRAM/SAM files
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Structure: [ val(meta), path(bam) ]
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pattern: "*.{bam/cram/sam}"
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## TODO nf-core: List all of the channels used as output with a descriptions and their structure
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output:
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- bam:
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type: file
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description: |
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Channel containing BAM files
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Structure: [ val(meta), path(bam) ]
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pattern: "*.bam"
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- bai:
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type: file
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description: |
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Channel containing indexed BAM (BAI) files
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Structure: [ val(meta), path(bai) ]
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pattern: "*.bai"
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- csi:
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type: file
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description: |
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Channel containing CSI files
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Structure: [ val(meta), path(csi) ]
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pattern: "*.csi"
42+
- versions:
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type: file
44+
description: |
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File containing software versions
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Structure: [ path(versions.yml) ]
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pattern: "versions.yml"
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authors:
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- "@CaroAMN"
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maintainers:
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- "@CaroAMN"

‎subworkflows/local/numorph_preprocessing/tests/main.nf.test‎

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nextflow_workflow {
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name "Test Subworkflow NUMORPH_PREPROCESSING"
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script "../main.nf"
5+
workflow "NUMORPH_PREPROCESSING"
6+
7+
tag "subworkflows"
8+
tag "subworkflows_"
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tag "subworkflows/numorph_preprocessing"
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tag "numorph"
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tag "numorph preprocessing"
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tag "numorph intensity"
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tag "numorph align"
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tag "numorph stitch"
15+
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17+
test("Numorph Preprocessing") {
18+
options "-stub"
19+
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when {
21+
workflow {
22+
"""
23+
input[0] = Channel.fromList([
24+
tuple([ id:'TEST1'],
25+
file('/home/schwitalla/Documents/test-datasets/test_data/images'),
26+
file('test-datasets/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
27+
])
28+
"""
29+
}
30+
}
31+
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then {
33+
assertAll(
34+
{ assert workflow.success},
35+
{ assert snapshot(workflow.out).match()}
36+
)
37+
}
38+
}
39+
}

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