From 9a8bba5910982ae637dedb8664e3121db77e173f Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 31 Jul 2024 08:49:07 +1200 Subject: [PATCH] Updated test data paths batch 6 (#6060) * Updated test data paths batch 6 * Update main.nf Add process_high_memory back --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- modules/nf-core/cutadapt/tests/main.nf.test | 6 +- modules/nf-core/gt/gff3/tests/main.nf.test | 2 +- .../gt/gff3validator/tests/main.nf.test | 16 +-- .../nf-core/gt/ltrharvest/tests/main.nf.test | 25 ++-- .../gt/ltrharvest/tests/main.nf.test.snap | 46 +++----- modules/nf-core/gt/stat/tests/main.nf.test | 4 +- .../gt/suffixerator/tests/main.nf.test | 24 ++-- modules/nf-core/oatk/tests/main.nf.test | 36 +++--- modules/nf-core/oatk/tests/main.nf.test.snap | 82 ++++++------- modules/nf-core/pycoqc/tests/main.nf.test | 2 +- modules/nf-core/trinity/tests/main.nf.test | 60 +++++----- .../nf-core/trinity/tests/main.nf.test.snap | 110 ++++++++++++++---- modules/nf-core/vcfanno/tests/main.nf.test | 22 ++-- tests/config/pytest_modules.yml | 3 - 14 files changed, 237 insertions(+), 201 deletions(-) diff --git a/modules/nf-core/cutadapt/tests/main.nf.test b/modules/nf-core/cutadapt/tests/main.nf.test index b7ea6ef9fe7..36927bd7fbe 100644 --- a/modules/nf-core/cutadapt/tests/main.nf.test +++ b/modules/nf-core/cutadapt/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { input[0] = [ [ id: 'test', single_end:true ], [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] """ @@ -47,8 +47,8 @@ nextflow_process { input[0] = [ [ id: 'test', single_end:false ], [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ] """ diff --git a/modules/nf-core/gt/gff3/tests/main.nf.test b/modules/nf-core/gt/gff3/tests/main.nf.test index cb44bc8ff60..46c7da35ba7 100644 --- a/modules/nf-core/gt/gff3/tests/main.nf.test +++ b/modules/nf-core/gt/gff3/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) ] """ } diff --git a/modules/nf-core/gt/gff3validator/tests/main.nf.test b/modules/nf-core/gt/gff3validator/tests/main.nf.test index 766e3e7425d..55184f84e46 100644 --- a/modules/nf-core/gt/gff3validator/tests/main.nf.test +++ b/modules/nf-core/gt/gff3validator/tests/main.nf.test @@ -16,13 +16,13 @@ nextflow_process { setup { run("GT_GFF3") { - script "../../../../nf-core/gt/gff3" + script "../../../gt/gff3" process { """ input[0] = [ [ id:'test' ], - file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) ] """ } @@ -40,9 +40,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, { assert path(process.out.success_log[0][1]).text.contains("input is valid GFF3") }, - { assert process.out.error_log == [] } + { assert process.out.error_log == [] }, + { assert snapshot(process.out).match() }, ) } @@ -57,7 +57,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) ] """ } @@ -79,7 +79,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_gff3'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gff3', checkIfExists: true) ] """ } @@ -88,9 +88,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert path(process.out.error_log[0][1]).text.contains("gt gff3validator: error:") }, { assert process.out.success_log == [] }, - { assert path(process.out.error_log[0][1]).text.contains("gt gff3validator: error:") } + { assert snapshot(process.out).match() }, ) } diff --git a/modules/nf-core/gt/ltrharvest/tests/main.nf.test b/modules/nf-core/gt/ltrharvest/tests/main.nf.test index ec3ba85f83d..f9e1ce13546 100644 --- a/modules/nf-core/gt/ltrharvest/tests/main.nf.test +++ b/modules/nf-core/gt/ltrharvest/tests/main.nf.test @@ -21,7 +21,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] input[1] = 'dna' """ @@ -40,8 +40,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } @@ -59,7 +58,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] input[1] = 'dna' """ @@ -78,8 +77,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } @@ -97,7 +95,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] input[1] = 'dna' """ @@ -116,8 +114,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } @@ -132,7 +129,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] """ } @@ -141,8 +138,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } @@ -158,7 +154,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] """ } @@ -167,8 +163,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/gt/ltrharvest/tests/main.nf.test.snap b/modules/nf-core/gt/ltrharvest/tests/main.nf.test.snap index a2f30278257..3f48b6e60db 100644 --- a/modules/nf-core/gt/ltrharvest/tests/main.nf.test.snap +++ b/modules/nf-core/gt/ltrharvest/tests/main.nf.test.snap @@ -11,25 +11,25 @@ ] ], "1": [ - + ], "2": [ - + ], "3": [ - + ], "4": [ "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37" ], "fasta": [ - + ], "gff3": [ - + ], "inner_fasta": [ - + ], "tabout": [ [ @@ -46,14 +46,6 @@ ], "timestamp": "2024-01-16T09:42:10.114754" }, - "versions": { - "content": [ - [ - "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37" - ] - ], - "timestamp": "2024-01-17T11:12:11.954224" - }, "stub": { "content": [ { @@ -66,25 +58,25 @@ ] ], "1": [ - + ], "2": [ - + ], "3": [ - + ], "4": [ "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37" ], "fasta": [ - + ], "gff3": [ - + ], "inner_fasta": [ - + ], "tabout": [ [ @@ -105,7 +97,7 @@ "content": [ { "0": [ - + ], "1": [ [ @@ -159,7 +151,7 @@ ] ], "tabout": [ - + ], "versions": [ "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37" @@ -172,7 +164,7 @@ "content": [ { "0": [ - + ], "1": [ [ @@ -226,7 +218,7 @@ ] ], "tabout": [ - + ], "versions": [ "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37" @@ -239,7 +231,7 @@ "content": [ { "0": [ - + ], "1": [ [ @@ -293,7 +285,7 @@ ] ], "tabout": [ - + ], "versions": [ "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37" @@ -302,4 +294,4 @@ ], "timestamp": "2024-01-17T11:20:13.665071" } -} \ No newline at end of file +} diff --git a/modules/nf-core/gt/stat/tests/main.nf.test b/modules/nf-core/gt/stat/tests/main.nf.test index d1fe2f0d734..5813b540120 100644 --- a/modules/nf-core/gt/stat/tests/main.nf.test +++ b/modules/nf-core/gt/stat/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = Channel.of( "##gff-version 3" + - file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true).text.toLowerCase() + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true).text.toLowerCase() ) .collectFile(name: 'sample.gff3', newLine: true) .map { file -> [ [ id:'test' ], file ] } @@ -43,7 +43,7 @@ nextflow_process { """ input[0] = [ [ id: 'test' ], - file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) ] """ } diff --git a/modules/nf-core/gt/suffixerator/tests/main.nf.test b/modules/nf-core/gt/suffixerator/tests/main.nf.test index 6a7079a912c..3f8fb5dd512 100644 --- a/modules/nf-core/gt/suffixerator/tests/main.nf.test +++ b/modules/nf-core/gt/suffixerator/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[1] = 'dna' """ @@ -28,8 +28,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } @@ -42,7 +41,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ] input[1] = 'protein' """ @@ -52,8 +51,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } @@ -68,7 +66,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[1] = 'dna' """ @@ -78,8 +76,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } @@ -94,7 +91,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[1] = 'protein' """ @@ -104,8 +101,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } @@ -118,7 +114,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[1] = 'xyz' """ @@ -143,7 +139,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[1] = 'xyz' """ diff --git a/modules/nf-core/oatk/tests/main.nf.test b/modules/nf-core/oatk/tests/main.nf.test index 7061ac7148f..88d87a7e843 100644 --- a/modules/nf-core/oatk/tests/main.nf.test +++ b/modules/nf-core/oatk/tests/main.nf.test @@ -19,8 +19,8 @@ nextflow_process { } process { """ - input[0] = Channel.of([[id:"ilDeiPorc1"],file(params.test_data['deilephila_porcellus']['mito']['hifi_reads'], checkIfExists: true)]) - + input[0] = Channel.of([[id:"ilDeiPorc1"],file(params.modules_testdata_base_path + 'genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa', checkIfExists: true)]) + hmm = file("https://raw.githubusercontent.com/c-zhou/OatkDB/main/v20230921/insecta_mito.fam", checkIfExists: true) hmm_h3f = file("https://github.com/c-zhou/OatkDB/raw/main/v20230921/insecta_mito.fam.h3f", checkIfExists: true) hmm_h3i = file("https://github.com/c-zhou/OatkDB/raw/main/v20230921/insecta_mito.fam.h3i", checkIfExists: true) @@ -29,24 +29,27 @@ nextflow_process { input[1] = Channel.of([hmm, hmm_h3f, hmm_h3i, hmm_h3m, hmm_h3p]) input[2] = [[],[],[],[],[]] """ - } + } } then { assertAll( { assert process.success }, - { assert snapshot(process.out.mito_fasta).match("mito_fasta") }, { assert process.out.final_gfa.get(0).get(1) ==~ '.*utg.final.gfa' } , - { assert snapshot(process.out.mito_bed).match("mito_bed") }, - { assert snapshot(process.out.mito_gfa).match("mito_gfa") }, { assert process.out.initial_gfa.get(0).get(1) ==~ '.*utg.gfa' } , { assert process.out.annot_mito_txt[0][1] ==~ ".*annot_mito.txt" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot( + process.out.mito_bed, + process.out.mito_fasta, + process.out.mito_gfa, + process.out.versions + ).match() + } ) } } - + test("test_oatk_pltd") { tag "test_oatk_pltd" @@ -57,8 +60,8 @@ nextflow_process { } process { """ - input[0] = Channel.of([[id:"ddAraThal4"],file(params.test_data['arabidopsis_thaliana']['plastid']['hifi_reads'], checkIfExists: true)]) - + input[0] = Channel.of([[id:"ddAraThal4"],file(params.modules_testdata_base_path + 'genomics/eukaryotes/arabidopsis_thaliana/plastid/ddAraThal4.HiFi.reads.fasta', checkIfExists: true)]) + input[1] = [[],[],[],[],[]] hmm = file("https://github.com/c-zhou/OatkDB/raw/main/v20230921/embryophyta_pltd.fam", checkIfExists: true) hmm_h3f = file("https://github.com/c-zhou/OatkDB/raw/main/v20230921/embryophyta_pltd.fam.h3f", checkIfExists: true) @@ -67,19 +70,22 @@ nextflow_process { hmm_h3p = file("https://github.com/c-zhou/OatkDB/raw/main/v20230921/embryophyta_pltd.fam.h3p", checkIfExists: true) input[2] = Channel.of([hmm, hmm_h3f, hmm_h3i, hmm_h3m, hmm_h3p]) """ - } + } } then { assertAll( { assert process.success }, - { assert snapshot(process.out.pltd_fasta).match("pltd_fasta") }, { assert process.out.final_gfa.get(0).get(1) ==~ '.*utg.final.gfa' } , - { assert snapshot(process.out.pltd_bed).match("pltd_bed") }, - { assert snapshot(process.out.pltd_gfa).match("pltd_gfa") }, { assert process.out.initial_gfa.get(0).get(1) ==~ '.*utg.gfa' } , { assert process.out.annot_pltd_txt[0][1] ==~ ".*annot_pltd.txt" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot( + process.out.pltd_bed, + process.out.pltd_fasta, + process.out.pltd_gfa, + process.out.versions + ).match() + } ) } diff --git a/modules/nf-core/oatk/tests/main.nf.test.snap b/modules/nf-core/oatk/tests/main.nf.test.snap index 1fc056965bf..bef3545bb47 100644 --- a/modules/nf-core/oatk/tests/main.nf.test.snap +++ b/modules/nf-core/oatk/tests/main.nf.test.snap @@ -1,88 +1,74 @@ { - "mito_bed": { + "test_oatk_pltd": { "content": [ [ [ { - "id": "ilDeiPorc1" + "id": "ddAraThal4" }, - "ilDeiPorc1.mito.ctg.bed:md5,177c87cb89996306611f6e74dba2ff60" + "ddAraThal4.pltd.ctg.bed:md5,f5925e6ec605b83547b9c72fae6f7087" ] - ] - ], - "timestamp": "2024-01-22T11:28:03.325434126" - }, - "mito_gfa": { - "content": [ + ], [ [ { - "id": "ilDeiPorc1" + "id": "ddAraThal4" }, - "ilDeiPorc1.mito.gfa:md5,88a058195aad319f57a330acea5357c5" + "ddAraThal4.pltd.ctg.fasta:md5,88cf092fd935801029a26bf88f6063bf" ] - ] - ], - "timestamp": "2024-01-22T11:28:03.334475394" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,bc3c4d7a42644e2c0d71422677a7d915" - ] - ], - "timestamp": "2024-01-22T11:28:03.361579579" - }, - "mito_fasta": { - "content": [ + ], [ [ { - "id": "ilDeiPorc1" + "id": "ddAraThal4" }, - "ilDeiPorc1.mito.ctg.fasta:md5,822b20d9e8f13591cb3a7474fda97402" + "ddAraThal4.pltd.gfa:md5,9749ffa1ebbf6b71fd7c9e8b410d64d4" ] + ], + [ + "versions.yml:md5,bc3c4d7a42644e2c0d71422677a7d915" ] ], - "timestamp": "2024-01-22T11:28:03.305999918" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-30T16:28:09.782502" }, - "pltd_bed": { + "test_oatk_mito": { "content": [ [ [ { - "id": "ddAraThal4" + "id": "ilDeiPorc1" }, - "ddAraThal4.pltd.ctg.bed:md5,f5925e6ec605b83547b9c72fae6f7087" + "ilDeiPorc1.mito.ctg.bed:md5,177c87cb89996306611f6e74dba2ff60" ] - ] - ], - "timestamp": "2024-01-22T11:28:15.844572574" - }, - "pltd_gfa": { - "content": [ + ], [ [ { - "id": "ddAraThal4" + "id": "ilDeiPorc1" }, - "ddAraThal4.pltd.gfa:md5,9749ffa1ebbf6b71fd7c9e8b410d64d4" + "ilDeiPorc1.mito.ctg.fasta:md5,822b20d9e8f13591cb3a7474fda97402" ] - ] - ], - "timestamp": "2024-01-22T11:28:15.860281161" - }, - "pltd_fasta": { - "content": [ + ], [ [ { - "id": "ddAraThal4" + "id": "ilDeiPorc1" }, - "ddAraThal4.pltd.ctg.fasta:md5,88cf092fd935801029a26bf88f6063bf" + "ilDeiPorc1.mito.gfa:md5,88a058195aad319f57a330acea5357c5" ] + ], + [ + "versions.yml:md5,bc3c4d7a42644e2c0d71422677a7d915" ] ], - "timestamp": "2024-01-22T11:28:15.81801003" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-30T16:27:44.199733" } } \ No newline at end of file diff --git a/modules/nf-core/pycoqc/tests/main.nf.test b/modules/nf-core/pycoqc/tests/main.nf.test index afc15a98015..0df42e226b5 100644 --- a/modules/nf-core/pycoqc/tests/main.nf.test +++ b/modules/nf-core/pycoqc/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt', checkIfExists: true) ] """ diff --git a/modules/nf-core/trinity/tests/main.nf.test b/modules/nf-core/trinity/tests/main.nf.test index 49e89a57711..8717518bd87 100644 --- a/modules/nf-core/trinity/tests/main.nf.test +++ b/modules/nf-core/trinity/tests/main.nf.test @@ -16,8 +16,8 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ] """ @@ -27,13 +27,12 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") }, + { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN7_c0_g1_i1 len=299 path=[0:0-151 2:152-298]") }, { assert snapshot( process.out.versions - ).match("versions") - }, - { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") }, - { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN7_c0_g1_i1 len=299 path=[0:0-151 2:152-298]") } - + ).match() + } ) } } @@ -45,7 +44,7 @@ nextflow_process { input[0] = [ [ id:'test', single_end:true ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] ] """ @@ -55,12 +54,12 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") }, + { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN10_c0_g1_i1 len=534 path=[0:0-533]") }, { assert snapshot( process.out.versions - ).match("versions") + ).match() }, - { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") }, - { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN10_c0_g1_i1 len=534 path=[0:0-533]") } ) } } @@ -72,10 +71,10 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ] """ @@ -85,12 +84,12 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") }, + { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=225 path=[0:0-224]") }, { assert snapshot( process.out.versions - ).match("versions") - }, - { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") }, - { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=225 path=[0:0-224]") } + ).match() + } ) } @@ -103,8 +102,8 @@ nextflow_process { input[0] = [ [ id:'test', single_end:true ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] ] """ @@ -114,12 +113,12 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") }, + { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=268 path=[0:0-267]") }, { assert snapshot( process.out.versions - ).match("versions") - }, - { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") }, - { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=268 path=[0:0-267]") } + ).match() + } ) } } @@ -134,8 +133,8 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ] """ @@ -145,12 +144,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.transcript_fasta, - process.out.log - ).match() - }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/trinity/tests/main.nf.test.snap b/modules/nf-core/trinity/tests/main.nf.test.snap index d543fc4406e..61217a2e33d 100644 --- a/modules/nf-core/trinity/tests/main.nf.test.snap +++ b/modules/nf-core/trinity/tests/main.nf.test.snap @@ -1,33 +1,103 @@ { - "versions": { + "homo_sapiens-test_rnaseq-paired-multiple": { "content": [ [ "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb" ] ], - "timestamp": "2024-01-15T19:10:42.684367037" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-30T16:43:56.823365" }, - "homo_sapiens-test_rnaseq-stub": { + "homo_sapiens-test_rnaseq-single": { "content": [ [ - [ - { - "id": "test", - "single_end": false - }, - "test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], + "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-30T16:41:17.496781" + }, + "homo_sapiens-test_rnaseq-paired": { + "content": [ [ - [ - { - "id": "test", - "single_end": false - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-30T16:39:34.89455" + }, + "homo_sapiens-test_rnaseq-single-multiple": { + "content": [ + [ + "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb" ] ], - "timestamp": "2024-01-15T19:11:49.900582628" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-30T16:46:07.157559" + }, + "homo_sapiens-test_rnaseq-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb" + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "transcript_fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-30T16:46:18.056478" } -} \ No newline at end of file +} diff --git a/modules/nf-core/vcfanno/tests/main.nf.test b/modules/nf-core/vcfanno/tests/main.nf.test index b28431b2778..8bbcfd8942f 100644 --- a/modules/nf-core/vcfanno/tests/main.nf.test +++ b/modules/nf-core/vcfanno/tests/main.nf.test @@ -15,11 +15,11 @@ nextflow_process { """ input[0] = [ [ id:'test_compressed', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists:true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] - input[1] = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml', checkIfExists: true) input[2] = [] input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), @@ -45,11 +45,11 @@ nextflow_process { """ input[0] = [ [ id:'test_uncompressed', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), [], - file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists:true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] - input[1] = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml', checkIfExists: true) input[2] = [] input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), @@ -77,11 +77,11 @@ nextflow_process { """ input[0] = [ [ id:'test_compressed', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists:true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] - input[1] = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml', checkIfExists: true) input[2] = [] input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 7cb4e8555e1..e6529a07ed5 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1635,9 +1635,6 @@ transdecoder/longorf: transdecoder/predict: - modules/nf-core/transdecoder/predict/** - tests/modules/nf-core/transdecoder/predict/** -trinity: - - modules/nf-core/trinity/** - - tests/modules/nf-core/trinity/** truvari/bench: - modules/nf-core/truvari/bench/** - tests/modules/nf-core/truvari/bench/**