From 5a5049ff1ed5cb8e64e71de3f60b1957e83af120 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 23 Aug 2024 08:58:43 +1200 Subject: [PATCH 1/2] Added nf-test for ucsc/bigwigaverageoverbed --- .../bigwigaverageoverbed/tests/main.nf.test | 36 +++++++++++++++++++ .../tests/main.nf.test.snap | 35 ++++++++++++++++++ tests/config/pytest_modules.yml | 3 -- .../nf-core/ucsc/bigwigaverageoverbed/main.nf | 15 -------- .../ucsc/bigwigaverageoverbed/nextflow.config | 5 --- .../ucsc/bigwigaverageoverbed/test.yml | 9 ----- 6 files changed, 71 insertions(+), 32 deletions(-) create mode 100644 modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test create mode 100644 modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf delete mode 100644 tests/modules/nf-core/ucsc/bigwigaverageoverbed/nextflow.config delete mode 100644 tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test b/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test new file mode 100644 index 00000000000..931015223b2 --- /dev/null +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test @@ -0,0 +1,36 @@ + +nextflow_process { + + name "Test Process UCSC_BIGWIGAVERAGEOVERBED" + script "../main.nf" + process "UCSC_BIGWIGAVERAGEOVERBED" + + tag "modules" + tag "modules_nfcore" + tag "ucsc" + tag "ucsc/bigwigaverageoverbed" + + test("test-ucsc-bigwigaverageoverbed") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bigwig/test.bigwig', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test.snap b/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test.snap new file mode 100644 index 00000000000..ea8e73d01ac --- /dev/null +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test-ucsc-bigwigaverageoverbed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tab:md5,d92334d90353577571eaf777933dce9b" + ] + ], + "1": [ + "versions.yml:md5,6cd96f62eb8229c893477ae2fefc9a73" + ], + "tab": [ + [ + { + "id": "test" + }, + "test.tab:md5,d92334d90353577571eaf777933dce9b" + ] + ], + "versions": [ + "versions.yml:md5,6cd96f62eb8229c893477ae2fefc9a73" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T08:58:18.917224" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index b698856bbae..be9ea2d69d7 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1581,9 +1581,6 @@ truvari/bench: ucsc/bedtobigbed: - modules/nf-core/ucsc/bedtobigbed/** - tests/modules/nf-core/ucsc/bedtobigbed/** -ucsc/bigwigaverageoverbed: - - modules/nf-core/ucsc/bigwigaverageoverbed/** - - tests/modules/nf-core/ucsc/bigwigaverageoverbed/** ucsc/gtftogenepred: - modules/nf-core/ucsc/gtftogenepred/** - tests/modules/nf-core/ucsc/gtftogenepred/** diff --git a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf deleted file mode 100644 index 771bf066e8e..00000000000 --- a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../../modules/nf-core/ucsc/bigwigaverageoverbed/main.nf' - -workflow test_ucsc_bigwigaverageoverbed { - input = [ - [ id: 'test' ], // meta map - [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ] - ] - bigwig = file(params.test_data['sarscov2']['illumina']['test_bigwig'], checkIfExists: true) - - UCSC_BIGWIGAVERAGEOVERBED ( input, bigwig ) -} diff --git a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/nextflow.config b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml deleted file mode 100644 index f6fbf57d842..00000000000 --- a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: ucsc bigwigaverageoverbed test_ucsc_bigwigaverageoverbed - command: nextflow run ./tests/modules/nf-core/ucsc/bigwigaverageoverbed -entry test_ucsc_bigwigaverageoverbed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bigwigaverageoverbed/nextflow.config - tags: - - ucsc - - ucsc/bigwigaverageoverbed - files: - - path: output/ucsc/test.tab - md5sum: d92334d90353577571eaf777933dce9b - - path: output/ucsc/versions.yml From 663071cc59e18260ee8b089949541ffd6b2f69c0 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Fri, 23 Aug 2024 11:08:34 +0100 Subject: [PATCH 2/2] Update modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test Co-authored-by: Joon Klaps --- modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test b/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test index 931015223b2..927641103d1 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test @@ -10,7 +10,7 @@ nextflow_process { tag "ucsc" tag "ucsc/bigwigaverageoverbed" - test("test-ucsc-bigwigaverageoverbed") { + test("sarscov2-bed-bigwig") { when { process {