From e4e61bf24a6069b762c21d5f3649c91237163f86 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 16 Aug 2024 17:43:44 +1200 Subject: [PATCH] Updated test data paths batch42 (#6199) --- .../denoisereadcounts/tests/main.nf.test | 17 +++--- .../denoisereadcounts/tests/main.nf.test.snap | 7 ++- .../gatk4/reblockgvcf/tests/main.nf.test | 48 +++++++++-------- .../gatk4/reblockgvcf/tests/main.nf.test.snap | 27 ++++++---- .../gatk4/splitncigarreads/tests/main.nf.test | 42 +++++++++------ .../splitncigarreads/tests/main.nf.test.snap | 27 ++++++---- .../gatk4/svannotate/tests/main.nf.test | 53 ++++++++++--------- .../gatk4/svannotate/tests/main.nf.test.snap | 27 ++++++---- .../gatk4/svcluster/tests/main.nf.test | 20 +++---- .../gatk4/svcluster/tests/main.nf.test.snap | 9 ++-- modules/nf-core/mageck/mle/tests/main.nf.test | 10 ++-- 11 files changed, 171 insertions(+), 116 deletions(-) diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test index 35ad8f7913a..e5fef2a2a24 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test @@ -19,9 +19,9 @@ nextflow_process { script "../../preprocessintervals/main.nf" process { """ - input[0] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]) - input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]) + input[0] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) input[3] = [[],[]] input[4] = [[],[]] """ @@ -33,12 +33,12 @@ nextflow_process { """ intervals = GATK4_PREPROCESSINTERVALS.out.interval_list.map {meta, list -> list} input[0] = Channel.of( - [[ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)], + [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)], ) .combine( intervals) - input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]) - input[3] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) """ } } @@ -66,7 +66,8 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.standardized, - process.out.denoised + process.out.denoised, + process.out.versions ).match() } ) } diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap index 000283b3938..f35eb283db4 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap @@ -18,12 +18,15 @@ }, "test_denoisedCR.tsv:md5,f9e56b8e12b4dadc91a6d977fa79c6a8" ] + ], + [ + "versions.yml:md5,140780e1af7318cc9259b8970bc70c81" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-20T14:45:41.834159" + "timestamp": "2024-08-16T12:34:12.568925" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test index 8bd3d51e74c..55c65bbb22c 100644 --- a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test +++ b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test @@ -13,10 +13,10 @@ nextflow_process { when { process { """ - input[0] = [[ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), []] - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[0] = [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), []] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) input[4] = [] input[5] = [] """ @@ -27,9 +27,11 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.vcf.get(0).get(1)).name, - file(process.out.vcf.get(0).get(2)).name - ).match("test_gatk4_reblockgvcf") } + file(process.out.vcf[0][1]).name, + file(process.out.vcf[0][2]).name, + process.out.versions + ).match() + } ) } @@ -39,10 +41,10 @@ nextflow_process { when { process { """ - input[0] = [[ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)] - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[0] = [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) input[4] = [] input[5] = [] """ @@ -53,9 +55,11 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.vcf.get(0).get(1)).name, - file(process.out.vcf.get(0).get(2)).name - ).match("test_gatk4_reblockgvcf_intervals") } + file(process.out.vcf[0][1]).name, + file(process.out.vcf[0][2]).name, + process.out.versions + ).match() + } ) } @@ -68,10 +72,10 @@ nextflow_process { when { process { """ - input[0] = [[ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), []] - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[0] = [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), []] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) input[4] = [] input[5] = [] """ @@ -82,9 +86,11 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.vcf.get(0).get(1)).name, - file(process.out.vcf.get(0).get(2)).name - ).match("test_gatk4_reblockgvcf_stub") } + file(process.out.vcf[0][1]).name, + file(process.out.vcf[0][2]).name, + process.out.versions + ).match() + } ) } diff --git a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap index c3651005d8b..6121c3d208a 100644 --- a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap @@ -2,34 +2,43 @@ "test_gatk4_reblockgvcf_stub": { "content": [ "test.rb.g.vcf.gz", - "test.rb.g.vcf.gz.tbi" + "test.rb.g.vcf.gz.tbi", + [ + "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-14T15:38:51.810662542" + "timestamp": "2024-08-16T12:32:19.353113" }, "test_gatk4_reblockgvcf_intervals": { "content": [ "test.rb.g.vcf.gz", - "test.rb.g.vcf.gz.tbi" + "test.rb.g.vcf.gz.tbi", + [ + "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-14T15:38:29.970623625" + "timestamp": "2024-08-16T12:32:11.896391" }, "test_gatk4_reblockgvcf": { "content": [ "test.rb.g.vcf.gz", - "test.rb.g.vcf.gz.tbi" + "test.rb.g.vcf.gz.tbi", + [ + "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-14T15:38:01.110199615" + "timestamp": "2024-08-16T12:32:00.687676" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test index b49101263aa..7a5eee0929c 100644 --- a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test +++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test @@ -14,10 +14,10 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), []] - input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), []] + input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } } @@ -25,7 +25,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads") } + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.versions + ).match() + } ) } @@ -36,10 +40,10 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)] - input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)] + input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } } @@ -47,7 +51,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_intervals") } + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.versions + ).match() + } ) } @@ -60,10 +68,10 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), [], []] - input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [], []] + input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } } @@ -71,7 +79,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_stub") } + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.versions + ).match() + } ) } diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap index 3e581cebe75..5a3484539d9 100644 --- a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap @@ -1,32 +1,41 @@ { "test_gatk4_splitncigarreads_intervals": { "content": [ - "test.bam" + "test.bam", + [ + "versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-15T08:26:10.91960579" + "timestamp": "2024-08-16T12:29:41.948726" }, "test_gatk4_splitncigarreads_stub": { "content": [ - "test.bam" + "test.bam", + [ + "versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-15T08:26:32.322712467" + "timestamp": "2024-08-16T12:29:53.2252" }, "test_gatk4_splitncigarreads": { "content": [ - "test.bam" + "test.bam", + [ + "versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-15T08:25:53.532205456" + "timestamp": "2024-08-16T12:29:30.774423" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/svannotate/tests/main.nf.test b/modules/nf-core/gatk4/svannotate/tests/main.nf.test index 0b4274e28fb..57bdd7d77bb 100644 --- a/modules/nf-core/gatk4/svannotate/tests/main.nf.test +++ b/modules/nf-core/gatk4/svannotate/tests/main.nf.test @@ -17,9 +17,9 @@ nextflow_process { script "../../../manta/germline/main.nf" process { """ - input[0] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), [], []]) - input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]) + input[0] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], []]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) input[3] = [] """ } @@ -41,10 +41,11 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.annotated_vcf.get(0).get(1)).name, - process.out.index.get(0).get(1), - ) - .match("test_gatk4_svannotate") } + file(process.out.annotated_vcf[0][1]).name, + process.out.index[0][1], + process.out.versions + ).match() + } ) } } @@ -55,9 +56,9 @@ nextflow_process { script "../../../manta/germline/main.nf" process { """ - input[0] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), [], []]) - input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]) + input[0] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], []]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) input[3] = [] """ } @@ -68,9 +69,9 @@ nextflow_process { process { """ input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.combine(MANTA_GERMLINE.out.diploid_sv_vcf_tbi, by:0).map({ meta, vcf, tbi -> [ meta, vcf, tbi, [] ]}) - input[1] = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)) - input[2] = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)) - input[3] = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)) + input[1] = Channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) + input[2] = Channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)) + input[3] = Channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)) """ } } @@ -79,10 +80,11 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.annotated_vcf.get(0).get(1)).name, - process.out.index.get(0).get(1), - ) - .match("test_gatk4_svannotate_fasta") } + file(process.out.annotated_vcf[0][1]).name, + process.out.index[0][1], + process.out.versions + ).match() + } ) } @@ -94,9 +96,9 @@ nextflow_process { script "../../../manta/germline/main.nf" process { """ - input[0] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), [], []]) - input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]) + input[0] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], []]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) input[3] = [] """ } @@ -106,7 +108,7 @@ nextflow_process { when { process { """ - ch_bed = Channel.of([[ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]) + ch_bed = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)]) input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.combine(MANTA_GERMLINE.out.diploid_sv_vcf_tbi, by:0).combine(ch_bed, by:0) input[1] = [] @@ -120,10 +122,11 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.annotated_vcf.get(0).get(1)).name, - process.out.index.get(0).get(1), - ) - .match("test_gatk4_svannotate_bed") } + file(process.out.annotated_vcf[0][1]).name, + process.out.index[0][1], + process.out.versions + ).match() + } ) } diff --git a/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap b/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap index 3cd5f971640..964713f6e1f 100644 --- a/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap @@ -2,34 +2,43 @@ "test_gatk4_svannotate_fasta": { "content": [ "test.vcf.gz", - "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4" + "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4", + [ + "versions.yml:md5,b08053927c0e51e8282586167122f4a5" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-15T09:13:17.256430039" + "timestamp": "2024-08-16T12:20:23.838882" }, "test_gatk4_svannotate": { "content": [ "test.vcf.gz", - "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4" + "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4", + [ + "versions.yml:md5,b08053927c0e51e8282586167122f4a5" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-15T09:12:54.263978543" + "timestamp": "2024-08-16T12:19:52.092072" }, "test_gatk4_svannotate_bed": { "content": [ "test.vcf.gz", - "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4" + "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4", + [ + "versions.yml:md5,b08053927c0e51e8282586167122f4a5" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-15T09:13:40.462621184" + "timestamp": "2024-08-16T12:20:54.131536" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/svcluster/tests/main.nf.test b/modules/nf-core/gatk4/svcluster/tests/main.nf.test index 5adb103fa8c..6f190f758f3 100644 --- a/modules/nf-core/gatk4/svcluster/tests/main.nf.test +++ b/modules/nf-core/gatk4/svcluster/tests/main.nf.test @@ -17,9 +17,9 @@ nextflow_process { script "../../../manta/germline/main.nf" process { """ - input[0] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), [], []]) - input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]) + input[0] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], []]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) input[3] = [] """ } @@ -31,9 +31,9 @@ nextflow_process { """ input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.combine(MANTA_GERMLINE.out.diploid_sv_vcf_tbi, by: 0) input[1] = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/svcluster/samples_ploidy.tsv", checkIfExists:true) - input[2] = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)) - input[3] = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)) - input[4] = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)) + input[2] = Channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) + input[3] = Channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)) + input[4] = Channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)) """ } } @@ -42,9 +42,11 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.clustered_vcf.get(0).get(1)).name, - process.out.clustered_vcf_index.get(0).get(1), - ).match("test_gatk4_svcluster") } + file(process.out.clustered_vcf[0][1]).name, + process.out.clustered_vcf_index[0][1], + process.out.versions + ).match() + } ) } } diff --git a/modules/nf-core/gatk4/svcluster/tests/main.nf.test.snap b/modules/nf-core/gatk4/svcluster/tests/main.nf.test.snap index 365ca28e810..fbf5cff04c5 100644 --- a/modules/nf-core/gatk4/svcluster/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/svcluster/tests/main.nf.test.snap @@ -2,12 +2,15 @@ "test_gatk4_svcluster": { "content": [ "test.vcf.gz", - "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4" + "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4", + [ + "versions.yml:md5,9c1678d540b64d057683488a4e91a45c" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-15T09:58:39.264182036" + "timestamp": "2024-08-16T12:18:12.769561" } } \ No newline at end of file diff --git a/modules/nf-core/mageck/mle/tests/main.nf.test b/modules/nf-core/mageck/mle/tests/main.nf.test index 5b20fd44d38..f6d06280485 100644 --- a/modules/nf-core/mageck/mle/tests/main.nf.test +++ b/modules/nf-core/mageck/mle/tests/main.nf.test @@ -16,11 +16,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['mus_musculus']['csv']['count_table'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) ] input[1] = - file(params.test_data['mus_musculus']['txt']['design_matrix'], - checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/design_matrix.txt', checkIfExists: true) """ } } @@ -46,11 +45,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['mus_musculus']['csv']['count_table'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) ] input[1] = - file(params.test_data['mus_musculus']['txt']['design_matrix'], - checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/design_matrix.txt', checkIfExists: true) """ } }