diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test b/modules/nf-core/narfmap/align/tests/main.nf.test index 10b3f4d0e29..a55cf5bf35c 100644 --- a/modules/nf-core/narfmap/align/tests/main.nf.test +++ b/modules/nf-core/narfmap/align/tests/main.nf.test @@ -43,9 +43,8 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.versions, - file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, + process.out.versions, ).match() } ) @@ -87,9 +86,8 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.versions, - file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, + process.out.versions, ).match() } ) @@ -134,9 +132,8 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.versions, - file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, + process.out.versions, ).match() } ) @@ -181,9 +178,8 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.versions, - file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, + process.out.versions, ).match() } ) @@ -228,9 +224,8 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.versions, - file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, + process.out.versions, ).match() } ) @@ -276,14 +271,11 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.versions, - file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, + process.out.versions, ).match() } ) } - } - } diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test.snap b/modules/nf-core/narfmap/align/tests/main.nf.test.snap index 09013b98931..527a6df508c 100644 --- a/modules/nf-core/narfmap/align/tests/main.nf.test.snap +++ b/modules/nf-core/narfmap/align/tests/main.nf.test.snap @@ -10,10 +10,6 @@ "test.bam:md5,5c407c8e621fc931af17a585526598bf" ] ], - [ - "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" - ], - "test.bam", [ "decompHashTableCtxInit...", "decompHashTableHeader...", @@ -21,13 +17,16 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-08T11:45:10.095839411" + "timestamp": "2024-07-08T12:31:24.171738358" }, "sarscov2 - [fastq1, fastq2], hashtable, true - stub": { "content": [ @@ -41,18 +40,17 @@ ] ], [ - "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" + ], - "test.bam", [ - + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-08T11:45:22.364107512" + "timestamp": "2024-07-08T12:31:44.736492735" }, "sarscov2 - fastq, hashtable, false": { "content": [ @@ -65,10 +63,6 @@ "test.bam:md5,ea3a6f419b6c8f91e99603058c608124" ] ], - [ - "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" - ], - "test.bam", [ "decompHashTableCtxInit...", "decompHashTableHeader...", @@ -76,13 +70,16 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-08T11:43:57.96792573" + "timestamp": "2024-07-08T12:19:58.278501718" }, "sarscov2 - fastq, hashtable, true": { "content": [ @@ -95,10 +92,6 @@ "test.bam:md5,e2632fce5442e05210edd516715489c4" ] ], - [ - "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" - ], - "test.bam", [ "decompHashTableCtxInit...", "decompHashTableHeader...", @@ -106,13 +99,16 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-08T11:44:17.486586239" + "timestamp": "2024-07-08T12:20:22.893500585" }, "sarscov2 - [fastq1, fastq2], hashtable, false": { "content": [ @@ -125,10 +121,6 @@ "test.bam:md5,ef0c12ae27778b906fd4f822ef7ce074" ] ], - [ - "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" - ], - "test.bam", [ "decompHashTableCtxInit...", "decompHashTableHeader...", @@ -136,13 +128,16 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-08T11:44:48.178604348" + "timestamp": "2024-07-08T12:20:54.147168602" }, "sarscov2 - [fastq1, fastq2], hashtable, true": { "content": [ @@ -155,10 +150,6 @@ "test.bam:md5,54965e6a11a9c31b1ae3c7e896c96c32" ] ], - [ - "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" - ], - "test.bam", [ "decompHashTableCtxInit...", "decompHashTableHeader...", @@ -166,12 +157,15 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-08T11:44:55.858525101" + "timestamp": "2024-07-08T12:21:06.378368579" } } \ No newline at end of file diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test b/modules/nf-core/narfmap/align/tests/segfault.nf.test index 3e89e97f37d..05ef3c9b530 100644 --- a/modules/nf-core/narfmap/align/tests/segfault.nf.test +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test @@ -10,7 +10,8 @@ nextflow_process { tag "narfmap/hashtable" tag "bug" - test("This should segfault") { + // https://github.com/bioinformaticsorphanage/NARFMAP/issues/10 + test("This should NOT segfault") { setup { run("NARFMAP_HASHTABLE") { @@ -44,9 +45,8 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.versions, - file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, + process.out.versions, ).match() } ) diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap b/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap index 9708b4ec130..2e1b8f4ca9e 100644 --- a/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap @@ -1,5 +1,5 @@ { - "This should segfault": { + "This should NOT segfault": { "content": [ [ [ @@ -10,10 +10,6 @@ "test.bam:md5,c38463b4da3a56010093cf2ce7634b86" ] ], - [ - "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" - ], - "test.bam", [ "decompHashTableCtxInit...", "decompHashTableHeader...", @@ -21,12 +17,15 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-08T11:46:14.084669293" + "timestamp": "2024-07-08T12:32:26.897477754" } } \ No newline at end of file