diff --git a/tests/data/bam/HG002.bam b/tests/data/bam/HG002.bam new file mode 100644 index 0000000..c7aead8 Binary files /dev/null and b/tests/data/bam/HG002.bam differ diff --git a/tests/mitocalling.nf.test b/tests/mitocalling.nf.test index 7c36514..19ab226 100644 --- a/tests/mitocalling.nf.test +++ b/tests/mitocalling.nf.test @@ -47,7 +47,7 @@ nextflow_pipeline { when { params { project = "test-job" - files = "$projectDir/tests/data/bam/*.bam" + files = "$projectDir/tests/data/bam/HG00096*.bam" mode = "mutect2" output = "out" output_reports = "reports" @@ -155,4 +155,28 @@ nextflow_pipeline { } + test("Run sample without readgroup an mutect2") { + + setup { + DownloadUtil.downloadAndExtractZip("https://mitoverse.i-med.ac.at/downloads/6-samples.zip", "${launchDir}/input") + } + + when { + params { + project = "test-job" + files = "$projectDir/tests/data/bam/HG002.bam" + mode = "mutect2" + output = "out" + output_reports = "reports" + output_auxiliary = "files" + } + } + + then { + assert workflow.success + assert snapshot(path("${launchDir}/out/variants.annotated.txt"),workflow.trace).match() + } + + } + } \ No newline at end of file diff --git a/tests/mitocalling.nf.test.snap b/tests/mitocalling.nf.test.snap index 6989d77..547c6da 100644 --- a/tests/mitocalling.nf.test.snap +++ b/tests/mitocalling.nf.test.snap @@ -74,6 +74,21 @@ }, "timestamp": "2024-03-07T23:06:50.681516749" }, + "Run sample without readgroup an mutect2": { + "content": [ + "variants.annotated.txt:md5,0fea21d7e7fc9881a2c959f1ca0c0923", + { + "tasksFailed": 0, + "tasksCount": 10, + "tasksSucceeded": 10 + } + ], + "meta": { + "nf-test": "0.9.0-rc1", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-29T12:04:01.840857" + }, "Runs with 6 samples provided as testdata with mutserve": { "content": [ "variants.annotated.txt:md5,4f06be3759a04ff20fa189dd9f5d2685",