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qclayssenqclayssen
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tentative switch to nf-test
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+110
-79
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6 files changed

+110
-79
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‎modules/nf-core/oncocnv/main.nf

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@@ -27,6 +27,7 @@ process ONCOCNV {
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def normal = normal.join(',')
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def tumor = tumor.join(',')
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def VERSION = '7.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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perl \$(which ONCOCNV_getCounts.pl) \\
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getControlStats \\
@@ -70,4 +71,22 @@ process ONCOCNV {
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r: \$(R --version | grep "R version" | sed 's/R version //g')
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END_VERSIONS
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"""
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stub:
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def VERSION = '7.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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// TODO add relevant files name
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"""
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touch stub.profile.png
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touch stub.profile.txt
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touch stub.summary.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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oncocnv: $VERSION
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perl: \$(perl --version | grep 'This is perl' | sed 's/.*(v//g' | sed 's/)//g')
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r: \$(R --version | grep "R version" | sed 's/R version //g')
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END_VERSIONS
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"""
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}

‎modules/nf-core/oncocnv/tests/main.nf.test

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@@ -0,0 +1,91 @@
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// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
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// nf-core modules test oncocnv
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nextflow_process {
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name "Test Process ONCOCNV"
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script "../main.nf"
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process "ONCOCNV"
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tag "modules"
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tag "modules_nfcore"
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tag "oncocnv"
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// TODO nf-core: Change the test name preferably indicating the test-data and file-format used
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test("sarscov2 - bam") {
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// TODO nf-core: If you are created a test for a chained module
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// (the module requires running more than one process to generate the required output)
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// add the 'setup' method here.
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// You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
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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', single_end:false], // meta map
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[
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true),
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]
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]
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input[1] = file(params.test_data['homo_sapiens']['genome']['genome_21_annotated_bed'], checkIfExists: true)
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input[2] = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists:true)
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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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//TODO nf-core: Add all required assertions to verify the test output.
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// See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
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)
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}
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}
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// TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
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test("sarscov2 - bam - 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', single_end:false], // meta map
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[
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true),
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]
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]
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input[1] = file(params.test_data['homo_sapiens']['genome']['genome_21_annotated_bed'], checkIfExists: true)
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input[2] = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists:true)
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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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//TODO nf-core: Add all required assertions to verify the test output.
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)
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}
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}
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}

‎tests/config/pytest_modules.yml

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@@ -206,9 +206,6 @@ nanomonsv/parse:
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ncbitools/vecscreen:
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- modules/nf-core/ncbitools/vecscreen/**
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- tests/modules/nf-core/ncbitools/vecscreen/**
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oncocnv:
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- modules/nf-core/oncocnv/**
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- tests/modules/nf-core/oncocnv/**
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paraclu:
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- modules/nf-core/paraclu/**
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- tests/modules/nf-core/paraclu/**

‎tests/modules/nf-core/oncocnv/main.nf

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This file was deleted.

‎tests/modules/nf-core/oncocnv/nextflow.config

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‎tests/modules/nf-core/oncocnv/test.yml

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