diff --git a/modules/nf-core/aria2/tests/main.nf.test b/modules/nf-core/aria2/tests/main.nf.test index ba033513e13e..641b136ad7c6 100644 --- a/modules/nf-core/aria2/tests/main.nf.test +++ b/modules/nf-core/aria2/tests/main.nf.test @@ -10,16 +10,17 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], // meta map - params.test_data['sarscov2']['illumina']['test_single_end_bam'] // https URL - ] + input[0] = [ + [ id:'test' ], + params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam' + ] """ } } then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -29,16 +30,17 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], // meta map - params.test_data['sarscov2']['illumina']['test_single_end_bam'] // https URL - ] + input[0] = [ + [ id:'test' ], + params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam' + ] """ } } then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/aria2/tests/main.nf.test.snap b/modules/nf-core/aria2/tests/main.nf.test.snap index 96911f6369b1..80cf6c8ea8c4 100644 --- a/modules/nf-core/aria2/tests/main.nf.test.snap +++ b/modules/nf-core/aria2/tests/main.nf.test.snap @@ -2,17 +2,6 @@ "sarscov2 Illumina single end [bam] - stub": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.single_end.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,1d3d763f0ff390b632205a498112b076" - ], "downloaded_file": [ [ { @@ -26,22 +15,15 @@ ] } ], - "timestamp": "2023-12-14T17:34:30.569759" + "timestamp": "2026-02-14T11:40:12.900794609", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 Illumina single end [bam]": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.single_end.bam:md5,21afed4c3e007de5e007cc5cbaebede7" - ] - ], - "1": [ - "versions.yml:md5,1d3d763f0ff390b632205a498112b076" - ], "downloaded_file": [ [ { @@ -55,6 +37,10 @@ ] } ], - "timestamp": "2023-12-14T17:34:22.216677" + "timestamp": "2026-02-14T11:40:06.798917586", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/consensus/tests/main.nf.test b/modules/nf-core/bcftools/consensus/tests/main.nf.test index aa20845982a9..64a6808aba3c 100644 --- a/modules/nf-core/bcftools/consensus/tests/main.nf.test +++ b/modules/nf-core/bcftools/consensus/tests/main.nf.test @@ -18,10 +18,10 @@ nextflow_process { """ input[0] = [ [ id:'test'], - 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']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], 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/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] """ } @@ -44,9 +44,9 @@ nextflow_process { """ input[0] = [ [ id:'test'], - 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']['genome']['genome_fasta'], 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/genome/genome.fasta', checkIfExists: true), [] ] """ @@ -70,11 +70,11 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // 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']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + [ id:'test' ], + 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/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] """ } diff --git a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test index f27136085728..e04ae2396610 100644 --- a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test +++ b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test @@ -26,7 +26,10 @@ nextflow_process { when { process { """ - input[0] = [ [id: 'test', single_end: true], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + input[0] = [ + [id: 'test', single_end: true], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] input[1] = UNTAR.out.untar.map{ it[1] } input[2] = true input[3] = true @@ -54,10 +57,11 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] + [id: 'test', single_end: false], + 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) + + ] input[1] = UNTAR.out.untar.map{ it[1] } input[2] = true input[3] = true @@ -86,7 +90,10 @@ nextflow_process { when { process { """ - input[0] = [ [id: 'test'], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] input[1] = UNTAR.out.untar.map{ it[1] } input[2] = true input[3] = true diff --git a/modules/nf-core/centrifuge/kreport/tests/main.nf.test b/modules/nf-core/centrifuge/kreport/tests/main.nf.test index 6d4bc6b1d2af..21c54b3fea48 100644 --- a/modules/nf-core/centrifuge/kreport/tests/main.nf.test +++ b/modules/nf-core/centrifuge/kreport/tests/main.nf.test @@ -25,7 +25,10 @@ nextflow_process { script "../../../centrifuge/centrifuge/main.nf" process { """ - input[0] = [ [id: 'test', single_end: true], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + input[0] = [ + [id: 'test', single_end: true], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] input[1] = UNTAR.out.untar.map{ it[1] } input[2] = true input[3] = true diff --git a/modules/nf-core/checkv/updatedatabase/tests/main.nf.test b/modules/nf-core/checkv/updatedatabase/tests/main.nf.test index 5a82c80e5391..0149c8ebf9c3 100644 --- a/modules/nf-core/checkv/updatedatabase/tests/main.nf.test +++ b/modules/nf-core/checkv/updatedatabase/tests/main.nf.test @@ -34,12 +34,10 @@ nextflow_process { } process { """ - input[0] = Channel.of( - [ - [ id: 'test' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - ) + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] input[1] = UNTAR.out.untar.map { it[1] } """ } @@ -71,12 +69,10 @@ nextflow_process { when { process { """ - input[0] = Channel.of( - [ - [ id: 'test' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - ) + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] input[1] = UNTAR.out.untar.map { it[1] } """ } diff --git a/modules/nf-core/decoupler/decoupler/tests/main.nf.test b/modules/nf-core/decoupler/decoupler/tests/main.nf.test index 8f1fcd21f70d..076520c2cc56 100644 --- a/modules/nf-core/decoupler/decoupler/tests/main.nf.test +++ b/modules/nf-core/decoupler/decoupler/tests/main.nf.test @@ -73,11 +73,11 @@ nextflow_process { """ input[0] = [ [ id: 'test', 'method_differential':'deseq2'], - file(params.test_data['generic']['tsv']['expression'], checkIfExists: true) + file(params.modules_testdata_base_path + 'generic/tsv/expression.tsv', checkIfExists: true) ] input[1] = [ ['id':'network'], - file(params.test_data['generic']['tsv']['network'], checkIfExists: true) + file(params.modules_testdata_base_path + 'generic/tsv/network.tsv', checkIfExists: true) ] input[2] = [ ['id':'annot'], @@ -126,11 +126,11 @@ nextflow_process { """ input[0] = [ [ id: 'test' ], - file(params.test_data['generic']['tsv']['expression'], checkIfExists: true) + file(params.modules_testdata_base_path + 'generic/tsv/expression.tsv', checkIfExists: true) ] input[1] = [ ['id':'network'], - file(params.test_data['generic']['tsv']['network'], checkIfExists: true) + file(params.modules_testdata_base_path + 'generic/tsv/network.tsv', checkIfExists: true) ] input[2] = [ ['id':'annot'], diff --git a/modules/nf-core/falco/tests/main.nf.test b/modules/nf-core/falco/tests/main.nf.test index 816c72ba2a8b..aeaa58547ffd 100644 --- a/modules/nf-core/falco/tests/main.nf.test +++ b/modules/nf-core/falco/tests/main.nf.test @@ -15,12 +15,7 @@ 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) ] ] """ } @@ -47,14 +42,8 @@ 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), ], ] """ @@ -81,12 +70,7 @@ nextflow_process { """ input[0] = [ [ id: 'test', single_end:false ], - [ - file( - params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], - checkIfExists: true - ), - ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)], ] """ } diff --git a/modules/nf-core/fast2q/tests/main.nf.test b/modules/nf-core/fast2q/tests/main.nf.test index b0f985f17797..aa68b90f11d4 100644 --- a/modules/nf-core/fast2q/tests/main.nf.test +++ b/modules/nf-core/fast2q/tests/main.nf.test @@ -61,7 +61,7 @@ nextflow_process { """ input[0] = [ [ id:'test1' ], // meta map - file(params.test_data_base + '/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true) // FASTQ file + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true) // FASTQ file ] input[1] = [ [ id:'library_name', multiple_features_per_read:false ], // meta map for second input @@ -99,12 +99,12 @@ nextflow_process { process { """ input[0] = [ - [ id:'test1' ], // meta map - file(params.test_data_base + '/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true) // FASTQ file + [ id:'test1' ], + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true) // FASTQ file ] input[1] = [ - [ id:'library_name', multiple_features_per_read:false ], // meta map for second input - file(params.test_data_base + '/data/genomics/mus_musculus/mageck/yusa_library.csv', checkIfExists: true) // library file + [ id:'library_name', multiple_features_per_read:false ], + file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/yusa_library.csv', checkIfExists: true) // library file ] """ } diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test index 5357712af23a..92d660f6f9af 100644 --- a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test +++ b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test @@ -16,10 +16,13 @@ nextflow_process { script "../../../bowtie2/build/main.nf" process { """ - input[0] = Channel.from([ - [[id: "sarscov2"], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)], - [[id: "human"] , file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)] - ]) + input[0] = channel.of([ + [id: "sarscov2"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ], [ + [id: "human"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ]) """ } } @@ -40,7 +43,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.database, process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } @@ -62,7 +65,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap index a485079b7d75..29c9f2781cbb 100644 --- a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap +++ b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap @@ -1,81 +1,42 @@ { "sarscov2 - human": { "content": [ - [ - [ - [ - "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf", - "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf", - "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", - "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626", - "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184", - "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597" - ], - [ - "genome.1.bt2:md5,2fbc8eeaf480f03b3a2362a782fa5755", - "genome.2.bt2:md5,a5300e3cf590d4cd8bd5521cac6337d6", - "genome.3.bt2:md5,d2a7a0e1c9891e847a15781c0695b84e", - "genome.4.bt2:md5,a55dc4b09e3e00586de6963800c95b9a", - "genome.rev.1.bt2:md5,93c07f7d04e5da6bf1322ad5f46ac806", - "genome.rev.2.bt2:md5,c3fa30132c0c9b9bc7868059e8e23466" - ], - "fastq_screen.conf:md5,ca56e866c7006a46bdfe4e751e787265" - ] - ], - [ - "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.02.1" - }, - "timestamp": "2025-03-25T12:58:36.506586801" - }, - "sarscov2 - human": { - "content": [ - [ - [ - [ - "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf", - "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf", - "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", - "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626", - "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184", - "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597" - ], + { + "database": [ [ - "genome.1.bt2:md5,2fbc8eeaf480f03b3a2362a782fa5755", - "genome.2.bt2:md5,a5300e3cf590d4cd8bd5521cac6337d6", - "genome.3.bt2:md5,d2a7a0e1c9891e847a15781c0695b84e", - "genome.4.bt2:md5,a55dc4b09e3e00586de6963800c95b9a", - "genome.rev.1.bt2:md5,93c07f7d04e5da6bf1322ad5f46ac806", - "genome.rev.2.bt2:md5,c3fa30132c0c9b9bc7868059e8e23466" - ], - "fastq_screen.conf:md5,ca56e866c7006a46bdfe4e751e787265" + [ + "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf", + "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf", + "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626", + "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184", + "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597" + ], + [ + "genome.1.bt2:md5,2fbc8eeaf480f03b3a2362a782fa5755", + "genome.2.bt2:md5,a5300e3cf590d4cd8bd5521cac6337d6", + "genome.3.bt2:md5,d2a7a0e1c9891e847a15781c0695b84e", + "genome.4.bt2:md5,a55dc4b09e3e00586de6963800c95b9a", + "genome.rev.1.bt2:md5,93c07f7d04e5da6bf1322ad5f46ac806", + "genome.rev.2.bt2:md5,c3fa30132c0c9b9bc7868059e8e23466" + ], + "fastq_screen.conf:md5,ca56e866c7006a46bdfe4e751e787265" + ] + ], + "versions": [ + "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c" ] - ], - [ - "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c" - ] + } ], + "timestamp": "2026-02-14T11:49:09.718820207", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-03-25T08:34:46.992911211" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - human - stub": { "content": [ { - "0": [ - [ - "fastq_screen.conf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c" - ], "database": [ [ "fastq_screen.conf:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -86,10 +47,10 @@ ] } ], + "timestamp": "2026-02-14T11:49:18.160638129", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-03-25T08:35:14.073325807" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test index 71230a224048..7c1d623ca5d8 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test +++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test @@ -19,10 +19,13 @@ nextflow_process { script "../../../bowtie2/build/main.nf" process { """ - input[0] = Channel.from([ - [[id: "sarscov2"], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)], - [[id: "human"] , file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)] - ]) + input[0] = channel.of([ + [id: "sarscov2"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ], [ + [id: "human"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ]) """ } } @@ -43,9 +46,10 @@ nextflow_process { when { process { """ - input[0] = [[ id:'test', single_end:true ], - [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] + input[0] = [ + [ id:'test', single_end:true ], + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ] input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database """ } @@ -68,9 +72,10 @@ nextflow_process { when { process { """ - input[0] = [[ id:'test', single_end:false ], - [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)] - ] + input[0] = [ + [ id:'test', single_end:false ], + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ] input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database """ } @@ -97,9 +102,10 @@ nextflow_process { when { process { """ - input[0] = [[ id:'test', single_end:true ], - [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] + input[0] = [ + [ id:'test', single_end:true ], + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ] input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database """ } diff --git a/modules/nf-core/ganon/buildcustom/tests/main.nf.test b/modules/nf-core/ganon/buildcustom/tests/main.nf.test index a5b3723242a1..6722d2406d78 100644 --- a/modules/nf-core/ganon/buildcustom/tests/main.nf.test +++ b/modules/nf-core/ganon/buildcustom/tests/main.nf.test @@ -19,9 +19,9 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - ] + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] input[1] = [] input[2] = [] input[3] = [] @@ -51,19 +51,22 @@ test("sarscov2 - genome - tsv") { process { """ input[0] = [ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), - ] - input[1] = ch_ganon_input_tsv = Channel.of(["genome.fasta", "Severe_acute_respiratory_syndrome_coronavirus_2", "2697049"]). - map { it.join("\t") } - .collectFile ( - name: "ganon_fasta_input.tsv", - newLine: true - ) + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = channel.of([ + "genome.fasta", + "Severe_acute_respiratory_syndrome_coronavirus_2", + "2697049" + ]).map { it.join("\t") } + .collectFile ( + name: "ganon_fasta_input.tsv", + newLine: true + ) input[2] = [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/prot_nodes.dmp', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/prot_names.dmp', checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/prot_nodes.dmp', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/prot_names.dmp', checkIfExists: true) + ] input[3] = [] """ } @@ -92,9 +95,9 @@ test("sarscov2 - genome - tsv") { process { """ input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - ] + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] input[1] = [] input[2] = [] input[3] = [] diff --git a/modules/nf-core/ganon/classify/tests/main.nf.test b/modules/nf-core/ganon/classify/tests/main.nf.test index c031e442d8b2..ad3c2cf159fc 100644 --- a/modules/nf-core/ganon/classify/tests/main.nf.test +++ b/modules/nf-core/ganon/classify/tests/main.nf.test @@ -17,9 +17,9 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - ] + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] input[1] = [] input[2] = [] input[3] = [] @@ -34,10 +34,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:true ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - ] + [ id:'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] input[1] = GANON_BUILDCUSTOM.out.db.map{it[1]} """ @@ -64,10 +62,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map + [ 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) ] ] input[1] = GANON_BUILDCUSTOM.out.db.map{it[1]} @@ -98,9 +96,9 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:true ], // meta map + [ 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) ] ] input[1] = [] diff --git a/modules/nf-core/gnu/sort/tests/main.nf.test b/modules/nf-core/gnu/sort/tests/main.nf.test index dbe473d276b1..9aef3daf12bc 100644 --- a/modules/nf-core/gnu/sort/tests/main.nf.test +++ b/modules/nf-core/gnu/sort/tests/main.nf.test @@ -16,10 +16,9 @@ nextflow_process { process { """ input[0] = [ - [id:'genome_test'], - file(params.test_data['generic']['unsorted_data']['unsorted_text']['genome_file'], - checkIfExists: true) - ] + [id:'genome_test'], + file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.genome', checkIfExists: true) + ] """ } } @@ -39,10 +38,9 @@ nextflow_process { process { """ input[0] = [ - [id:'test'], - file(params.test_data['generic']['unsorted_data']['unsorted_text']['intervals'], - checkIfExists: true) - ] + [id:'test'], + file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.bed', checkIfExists: true) + ] """ } } @@ -63,10 +61,9 @@ nextflow_process { process { """ input[0] = [ - [id:'test'], - file(params.test_data['generic']['unsorted_data']['unsorted_text']['numbers_csv'], - checkIfExists: true) - ] + [id:'test'], + file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.csv', checkIfExists: true) + ] """ } } @@ -88,10 +85,9 @@ nextflow_process { process { """ input[0] = [ - [id:'test'], - file(params.test_data['generic']['unsorted_data']['unsorted_text']['numbers_csv'], - checkIfExists: true) - ] + [id:'test'], + file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.csv', checkIfExists: true) + ] """ } } diff --git a/modules/nf-core/grabix/check/tests/main.nf.test b/modules/nf-core/grabix/check/tests/main.nf.test index c4a350d9b738..b3be35fa3f8c 100644 --- a/modules/nf-core/grabix/check/tests/main.nf.test +++ b/modules/nf-core/grabix/check/tests/main.nf.test @@ -12,10 +12,10 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ - [ id: 'test'], // meta map - [file(params.test_data_base + "/data/genomics/sarscov2/genome/genome.fasta.gz", checkIfExists: true) ] - ]) + input[0] = [ + [ id: 'test'], + [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) ] + ] """ } } diff --git a/modules/nf-core/graphtyper/genotype/main.nf b/modules/nf-core/graphtyper/genotype/main.nf index 875e590b6784..c4032fd69924 100644 --- a/modules/nf-core/graphtyper/genotype/main.nf +++ b/modules/nf-core/graphtyper/genotype/main.nf @@ -24,8 +24,8 @@ process GRAPHTYPER_GENOTYPE { script: def args = task.ext.args ?: '' def bam_path_text = bam.sort().join('\\n') - def region_text = region_file.size() > 0 ? "--region_file ${region_file}" : "" - if (region_file.size() == 0 && ! args.contains("region")) { + def region_text = region_file ? "--region_file ${region_file}" : "" + if (!region_file && ! args.contains("region")) { error "GRAPHTYPER_GENOTYPE requires either a region file or a region specified using '--region' in ext.args" } """ diff --git a/modules/nf-core/graphtyper/genotype/tests/main.nf.test b/modules/nf-core/graphtyper/genotype/tests/main.nf.test index 799369a11705..30341d65490c 100644 --- a/modules/nf-core/graphtyper/genotype/tests/main.nf.test +++ b/modules/nf-core/graphtyper/genotype/tests/main.nf.test @@ -29,7 +29,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } @@ -49,7 +49,7 @@ nextflow_process { ] input[1] = [ [ id: 'ref' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[2] = [ [ id: 'ref_index' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - input[3] = [] + input[3] = channel.of([]) """ } } @@ -57,7 +57,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + file(process.out.tbi[0][1]).name, + file(process.out.vcf[0][1]).name, // unstable + process.out.versions + ).match() } ) } @@ -75,7 +79,7 @@ nextflow_process { ] input[1] = [ [ id: 'ref' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[2] = [ [ id: 'ref_index' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - input[3] = file(params.test_data['sarscov2']['genome']['regions_txt'], checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/graphtyper/regions.txt', checkIfExists: true) """ } } @@ -83,7 +87,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/graphtyper/genotype/tests/main.nf.test.snap b/modules/nf-core/graphtyper/genotype/tests/main.nf.test.snap index 5825400ad871..ff7a29996ca5 100644 --- a/modules/nf-core/graphtyper/genotype/tests/main.nf.test.snap +++ b/modules/nf-core/graphtyper/genotype/tests/main.nf.test.snap @@ -1,81 +1,21 @@ { "multiple - region_args": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "000000001-000029829.vcf.gz:md5,0d1eb26e299eb31a29a98905c789c67a" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "000000001-000029829.vcf.gz.tbi:md5,b7fb6638f27d6221c9fbc8dae50ac70e" - ] - ], - "2": [ - "versions.yml:md5,131488e7eb93b8c761765afcbc51a719" - ], - "tbi": [ - [ - { - "id": "test" - }, - "000000001-000029829.vcf.gz.tbi:md5,b7fb6638f27d6221c9fbc8dae50ac70e" - ] - ], - "vcf": [ - [ - { - "id": "test" - }, - "000000001-000029829.vcf.gz:md5,0d1eb26e299eb31a29a98905c789c67a" - ] - ], - "versions": [ - "versions.yml:md5,131488e7eb93b8c761765afcbc51a719" - ] - } + "000000001-000029829.vcf.gz.tbi", + "000000001-000029829.vcf.gz", + [ + "versions.yml:md5,131488e7eb93b8c761765afcbc51a719" + ] ], + "timestamp": "2026-02-14T13:12:02.090140452", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" - }, - "timestamp": "2025-02-26T07:03:36.959598093" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "single - region_file": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - [ - "000000001-000029829.vcf.gz:md5,f8605372cfa504ad9797d87aaa63c7a2", - "000001000-000005000.vcf.gz:md5,c421cc18d462549c0866e84833e10ac5" - ] - ] - ], - "1": [ - [ - { - "id": "test" - }, - [ - "000000001-000029829.vcf.gz.tbi:md5,6cf39cb5edec1dad83e9bd85b68ae9d9", - "000001000-000005000.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905" - ] - ] - ], - "2": [ - "versions.yml:md5,131488e7eb93b8c761765afcbc51a719" - ], "tbi": [ [ { @@ -93,8 +33,8 @@ "id": "test" }, [ - "000000001-000029829.vcf.gz:md5,f8605372cfa504ad9797d87aaa63c7a2", - "000001000-000005000.vcf.gz:md5,c421cc18d462549c0866e84833e10ac5" + "000000001-000029829.vcf.gz:md5,25add251ebd7c81b8225b3ea95472d4e", + "000001000-000005000.vcf.gz:md5,7e847271d397305bbebe87e15eb1daf5" ] ] ], @@ -103,40 +43,15 @@ ] } ], + "timestamp": "2026-02-14T12:27:08.451782661", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" - }, - "timestamp": "2025-02-26T07:03:27.012690492" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "single - region_file - stub": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - [ - "region1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "region2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - [ - { - "id": "test" - }, - [ - "region1.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", - "region2.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "2": [ - "versions.yml:md5,131488e7eb93b8c761765afcbc51a719" - ], "tbi": [ [ { @@ -164,10 +79,10 @@ ] } ], + "timestamp": "2026-02-14T12:28:22.719581642", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" - }, - "timestamp": "2025-02-14T15:55:40.374911703" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/hamronization/rgi/tests/main.nf.test b/modules/nf-core/hamronization/rgi/tests/main.nf.test index d387067f3ee1..4bf7b51b5459 100644 --- a/modules/nf-core/hamronization/rgi/tests/main.nf.test +++ b/modules/nf-core/hamronization/rgi/tests/main.nf.test @@ -43,7 +43,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) ] input[1] = RGI_CARDANNOTATION.out.db input[2] = [] diff --git a/modules/nf-core/hlala/preparegraph/tests/main.nf.test b/modules/nf-core/hlala/preparegraph/tests/main.nf.test index ef3e57e36286..429e32a45cf5 100644 --- a/modules/nf-core/hlala/preparegraph/tests/main.nf.test +++ b/modules/nf-core/hlala/preparegraph/tests/main.nf.test @@ -20,17 +20,14 @@ nextflow_process { process { """ input[0] = [ - [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['genome']['prg_input'], checkIfExists: true) + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/PRG_test.zip', checkIfExists: true) ] """ } } } when { - params { - outdir = "$outputDir" - } process { """ input[0] = UNZIP.out.unzipped_archive.map{ meta, filepath -> @@ -41,8 +38,8 @@ nextflow_process { } then { - def stable_name = getAllFilesFromDir(outputDir, relative:true, includeDir: true) - def stable_content = getAllFilesFromDir(outputDir, ignore: ['**/referenceGenome.fa.{bwt,pac,sa}','**/referenceGenome.fa_bowtie2idx*']) + def stable_name = getAllFilesFromDir(outputDir, relative:true, includeDir: true) + def stable_content = getAllFilesFromDir(outputDir, ignore: ['**/referenceGenome.fa.{bwt,pac,sa}','**/referenceGenome.fa_bowtie2idx*']) assertAll( { assert process.success }, { assert snapshot(stable_name,stable_content).match() } @@ -62,8 +59,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['genome']['prg_input'], checkIfExists: true) + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/PRG_test.zip', checkIfExists: true) ] """ } diff --git a/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test b/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test index ff9eb040e350..4ef3434f9978 100644 --- a/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test +++ b/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test @@ -20,10 +20,10 @@ nextflow_process { input[0] =[ [id:"dict_test"], [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - 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/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) ] ] """ @@ -53,10 +53,10 @@ nextflow_process { input[0] =[ [id:"dict_stub"], [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - 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/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) ] ] """ diff --git a/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test b/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test index 2dc0a762f1fe..ba588c23dab2 100644 --- a/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test +++ b/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test @@ -23,9 +23,9 @@ nextflow_process { [], [] ] - input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] input[4] = [ [] , []] input[5] = [ [] , []] """ @@ -58,9 +58,9 @@ nextflow_process { [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] - input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] input[4] = [ [] , []] input[5] = [ [] , []] """ @@ -93,9 +93,9 @@ nextflow_process { [], [] ] - input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] input[4] = [ [] , []] input[5] = [ [] , []] """ diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test index 4fff3efc2669..62ec369d5ea3 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test +++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test @@ -22,9 +22,9 @@ nextflow_process { [], [] ] - input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } } @@ -54,9 +54,9 @@ nextflow_process { [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] - input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } } @@ -84,9 +84,9 @@ nextflow_process { [], [] ] - input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } } diff --git a/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test index d521219f0108..d75b2763ce9c 100644 --- a/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test +++ b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test @@ -22,7 +22,7 @@ nextflow_process { """ input[0] = [ [ id:'test', tumor_id:'tumour' ], - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), [], // index only needed if using intervals or tumor-normal calling [], [], @@ -30,7 +30,7 @@ nextflow_process { ] input[1] = [ // fasta [ id: 'reference' ], - 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[2] = [] // pon input[3] = [] // pon index @@ -65,16 +65,16 @@ nextflow_process { // """ // input[0] = [ // [ id:'test', tumor_id:'tumour', normal_id:'normal' ], - // file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - // file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), - // file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - // file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), // [] // ] // input[1] = [ // fasta // [ id: 'reference' ], //genomics/homo_sapiens/genome/chr21/sequence/genome.fasta // // file() - // 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[2] = [] // pon // input[3] = [] // pon index @@ -106,15 +106,15 @@ nextflow_process { // """ // input[0] = [ // [ id:'test', tumor_id:'tumor' ], - // file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - // file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), // [], // [], - // file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) // ] // input[1] = [ // fasta // [ id: 'reference' ], - // 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[2] = [] // pon // input[3] = [] // pon index @@ -149,15 +149,15 @@ nextflow_process { // """ // input[0] = [ // [ id:'test', tumor_id:'tumor', normal_id:'normal'], - // file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - // file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), - // file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - // file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), - // file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) // ] // input[1] = [ // fasta // [ id: 'reference' ], - // 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[2] = [] // pon // input[3] = [] // pon index @@ -192,18 +192,18 @@ nextflow_process { // """ // input[0] = [ // [ id:'test', tumor_id:'tumour' ], - // file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - // file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), // [], // [], - // file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) + // file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) // ] // input[1] = [ // fasta // [ id: 'reference' ], - // 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[2] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) - // input[3] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) + // input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) + // input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) // """ // } // } @@ -233,7 +233,7 @@ nextflow_process { """ input[0] = [ [ id:'test', tumor_id:'tumour' ], - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), [], // index only neeeded if using intervals or tumor-normal calling [], [], @@ -241,7 +241,7 @@ nextflow_process { ] input[1] = [ // fasta [ id: 'reference' ], - 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[2] = [] // pon input[3] = [] // pon index @@ -273,18 +273,18 @@ nextflow_process { """ input[0] = [ [ id:'test', tumor_id:'tumour' ], - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), [], [], - file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) ] input[1] = [ // fasta [ id: 'reference' ], - 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[2] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) """ } } diff --git a/modules/nf-core/pints/caller/tests/main.nf.test b/modules/nf-core/pints/caller/tests/main.nf.test index e0e2f8ea3f99..eb981756935b 100644 --- a/modules/nf-core/pints/caller/tests/main.nf.test +++ b/modules/nf-core/pints/caller/tests/main.nf.test @@ -79,8 +79,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) [], ] input[1] = "GROseq" diff --git a/modules/nf-core/proteus/readproteingroups/tests/main.nf.test b/modules/nf-core/proteus/readproteingroups/tests/main.nf.test index 468e868c00d1..7511080a9de4 100644 --- a/modules/nf-core/proteus/readproteingroups/tests/main.nf.test +++ b/modules/nf-core/proteus/readproteingroups/tests/main.nf.test @@ -18,7 +18,11 @@ nextflow_process { } process { """ - input[0] = [[ id:"fakeBatch" ], file(params.test_data['proteomics']['maxquant']['mq_samplesheet'], checkIfExists: true), file(params.test_data['proteomics']['maxquant']['mq_proteingroups'], checkIfExists: true)] + input[0] = [ + [ id:"fakeBatch" ], + file(params.modules_testdata_base_path + 'proteomics/maxquant/MaxQuant_samplesheet.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + 'proteomics/maxquant/MaxQuant_proteinGroups.txt', checkIfExists: true) + ] """ } } @@ -52,7 +56,11 @@ nextflow_process { } process { """ - input[0] = [[ id:"fakeBatch" ], file(params.test_data['proteomics']['maxquant']['mq_samplesheet'], checkIfExists: true), file(params.test_data['proteomics']['maxquant']['mq_proteingroups'], checkIfExists: true)] + input[0] = [ + [ id:"fakeBatch" ], + file(params.modules_testdata_base_path + 'proteomics/maxquant/MaxQuant_samplesheet.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + 'proteomics/maxquant/MaxQuant_proteinGroups.txt', checkIfExists: true) + ] """ } } diff --git a/modules/nf-core/rgi/main/tests/main.nf.test b/modules/nf-core/rgi/main/tests/main.nf.test index 1fca563a9694..fc4a5616f941 100644 --- a/modules/nf-core/rgi/main/tests/main.nf.test +++ b/modules/nf-core/rgi/main/tests/main.nf.test @@ -43,8 +43,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) ] input[1] = RGI_CARDANNOTATION.out.db input[2] = [] @@ -75,8 +75,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) ] input[1] = RGI_CARDANNOTATION.out.db input[2] = [] diff --git a/modules/nf-core/rmarkdownnotebook/tests/main.nf.test b/modules/nf-core/rmarkdownnotebook/tests/main.nf.test index 2657be7dfa52..839e57cc169d 100644 --- a/modules/nf-core/rmarkdownnotebook/tests/main.nf.test +++ b/modules/nf-core/rmarkdownnotebook/tests/main.nf.test @@ -16,7 +16,10 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test_rmd' ], file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) ] + input[0] = [ + [ id:'test_rmd' ], + file(params.modules_testdata_base_path + 'generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd', checkIfExists: true) + ] input[1] = [:] input[2] = [] """ @@ -45,9 +48,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test_rmd' ], file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) ] + input[0] = [ + [ id:'test_rmd' ], + file(params.modules_testdata_base_path + 'generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd', checkIfExists: true) + ] input[1] = [input_filename: "hello.txt", n_iter: 12] - input[2] = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) """ } } @@ -76,7 +82,10 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test_rmd' ], file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) ] + input[0] = [ + [ id:'test_rmd' ], + file(params.modules_testdata_base_path + 'generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd', checkIfExists: true) + ] input[1] = [:] input[2] = [] """ diff --git a/modules/nf-core/seqtk/mergepe/tests/main.nf.test b/modules/nf-core/seqtk/mergepe/tests/main.nf.test index b55ab3e626bd..ad90792628da 100644 --- a/modules/nf-core/seqtk/mergepe/tests/main.nf.test +++ b/modules/nf-core/seqtk/mergepe/tests/main.nf.test @@ -16,7 +16,7 @@ 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) ] """ } @@ -41,8 +41,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - [ 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) ] ] """ @@ -68,7 +69,7 @@ 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) ] """ } diff --git a/modules/nf-core/sylph/sketch/tests/main.nf.test b/modules/nf-core/sylph/sketch/tests/main.nf.test index c0520f937eee..c556d479cae4 100644 --- a/modules/nf-core/sylph/sketch/tests/main.nf.test +++ b/modules/nf-core/sylph/sketch/tests/main.nf.test @@ -12,10 +12,11 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + input[0] = [ + [ id:'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) """ } } @@ -32,11 +33,14 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + input[0] = [ + [ id:'test', single_end:false ], + [ + 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) + ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) """ } } @@ -56,11 +60,14 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + input[0] = [ + [ id:'test', single_end:false ], + [ + 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) + ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) """ } } diff --git a/modules/nf-core/sylph/sketchsamples/tests/main.nf.test b/modules/nf-core/sylph/sketchsamples/tests/main.nf.test index 3f68d0685982..7fe31041ab16 100644 --- a/modules/nf-core/sylph/sketchsamples/tests/main.nf.test +++ b/modules/nf-core/sylph/sketchsamples/tests/main.nf.test @@ -13,9 +13,9 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] + [ id:'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ] """ } } @@ -33,11 +33,12 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] + [ id:'test', single_end:false ], + [ + 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) + ] + ] """ } } @@ -57,10 +58,13 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] + input[0] = [ + [ id:'test', single_end:false ], + [ + 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/umitools/group/tests/main.nf.test b/modules/nf-core/umitools/group/tests/main.nf.test index 9ba95f871ea4..ce4c5564b370 100644 --- a/modules/nf-core/umitools/group/tests/main.nf.test +++ b/modules/nf-core/umitools/group/tests/main.nf.test @@ -20,10 +20,10 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map + [ 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) ] ] """ @@ -35,9 +35,9 @@ nextflow_process { process { """ input[0] = [ - [ id:'sarscov2'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] + [ id:'sarscov2'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] """ } } @@ -70,9 +70,10 @@ nextflow_process { when { process { """ - input[0] = [[ id:'test'], // meta map - file(params.test_data_base + '/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.test_data_base + '/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', 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] = true input[2] = true diff --git a/subworkflows/nf-core/differential_functional_enrichment/main.nf b/subworkflows/nf-core/differential_functional_enrichment/main.nf index 911e55eb1280..9950e1367319 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/main.nf +++ b/subworkflows/nf-core/differential_functional_enrichment/main.nf @@ -2,13 +2,13 @@ // // Perform enrichment analysis // -include { GPROFILER2_GOST } from "../../../modules/nf-core/gprofiler2/gost/main.nf" +include { GPROFILER2_GOST } from '../../../modules/nf-core/gprofiler2/gost/main.nf' include { CUSTOM_TABULARTOGSEAGCT } from '../../../modules/nf-core/custom/tabulartogseagct/main.nf' include { CUSTOM_TABULARTOGSEACLS } from '../../../modules/nf-core/custom/tabulartogseacls/main.nf' include { CUSTOM_TABULARTOGSEACHIP } from '../../../modules/nf-core/custom/tabulartogseachip/main.nf' include { GSEA_GSEA } from '../../../modules/nf-core/gsea/gsea/main.nf' -include { PROPR_GREA } from "../../../modules/nf-core/propr/grea/main.nf" -include { DECOUPLER_DECOUPLER } from '../../../modules/nf-core/decoupler/decoupler/main' +include { PROPR_GREA } from '../../../modules/nf-core/propr/grea/main.nf' +include { DECOUPLER_DECOUPLER } from '../../../modules/nf-core/decoupler/decoupler/main' // Combine meta maps, including merging non-identical values of shared keys (e.g. 'id') def mergeMaps(meta, meta2){ @@ -33,7 +33,7 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // Add method information into meta map of ch_input // This information is used later to determine which method to run for each input @@ -72,12 +72,12 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { // GSEA uses meta.variable, so only keep contrasts where meta.variable is present ch_contrasts_transposed = ch_contrasts.transpose() - .filter { meta, contrastMap, variable, reference, target, formula, comparison -> + .filter { _meta, _contrastMap, variable, _reference, _target, _formula, _comparison -> variable?.trim() } ch_input_for_gsea = ch_input - .filter{ it[4] == 'gsea' } + .filter{ it -> it[4] == 'gsea' } .combine(ch_samplesheet.join(ch_featuresheet), by:0) .combine(ch_contrasts_transposed, by:0) .multiMap(criteria) diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test index 077d3f06b9b6..6a09b83a9ece 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test @@ -30,7 +30,7 @@ nextflow_workflow { when { workflow { """ - ch_input = Channel.of([ + ch_input = channel.of([ ['id':'Condition_genotype_WT_KO', 'variable':'Condition genotype', 'reference':'WT', 'target':'KO', 'blocking':'batch'], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/Condition_genotype_WT_KO.deseq2.results_filtered.tsv", checkIfExists: true), [], @@ -39,9 +39,9 @@ nextflow_workflow { ]) input[0] = ch_input - input[1] = Channel.of([[], [], [], [], [], []]) - input[2] = Channel.of([[], []]) - input[3] = Channel.of([ + input[1] = channel.of([[], [], [], [], [], []]) + input[2] = channel.of([[], []]) + input[3] = channel.of([ ['id':'Condition_genotype_WT_KO', 'variable':'Condition genotype', 'reference':'WT', 'target':'KO', 'blocking':'batch'], [], // '', // @@ -83,19 +83,19 @@ nextflow_workflow { ] // Define inputs - ch_samplesheet = Channel.of([ + ch_samplesheet = channel.of([ [ id:'test' ], file(testData.expression_test_data_dir + testData.samplesheet_file) ]) - ch_transcript_lengths = Channel.of([ [], [] ]) - ch_control_features = Channel.of([ [], [] ]) - ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file)) + ch_transcript_lengths = channel.of([ [], [] ]) + ch_control_features = channel.of([ [], [] ]) + ch_contrasts = channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file)) .splitCsv ( header:true, sep:',' ) .map{ tuple([id: 'test'], it, it.variable, it.reference, it.target, it.formula, it.comparison) } .groupTuple() - ch_input = Channel.of([ + ch_input = channel.of([ [ id:'test' ], file(testData.expression_test_data_dir + testData.abundance_file), 'deseq2', // analysis method @@ -127,8 +127,8 @@ nextflow_workflow { } input[0] = ch_input - input[1] = Channel.of([[], [], [], [], [], []]) - input[2] = Channel.of([[], []]) + input[1] = channel.of([[], [], [], [], [], []]) + input[2] = channel.of([[], []]) input[3] = ch_featuresheet """ } @@ -158,7 +158,7 @@ nextflow_workflow { workflow { """ // Define test data - def testData = [ + def testDataSetup = [ expression_test_data_dir: params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/', contrasts_file: 'SRP254919.contrasts.csv', abundance_file: 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', @@ -166,21 +166,21 @@ nextflow_workflow { ] // Define inputs - ch_samplesheet = Channel.of([ + ch_samplesheet = channel.of([ [ id:'test' ], - file(testData.expression_test_data_dir + testData.samplesheet_file) + file(testDataSetup.expression_test_data_dir + testDataSetup.samplesheet_file) ]) - ch_transcript_lengths = Channel.of([ [], [] ]) - ch_control_features = Channel.of([ [], [] ]) - ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file)) + ch_transcript_lengths = channel.of([ [], [] ]) + ch_control_features = channel.of([ [], [] ]) + ch_contrasts = channel.fromPath(file(testDataSetup.expression_test_data_dir + testDataSetup.contrasts_file)) .splitCsv ( header:true, sep:',' ) .map{ tuple([ id:'test' ], it, it.variable, it.reference, it.target, it.formula, it.comparison) } .groupTuple() - ch_input = Channel.of([ + ch_input = channel.of([ [ id:'test' ], - file(testData.expression_test_data_dir + testData.abundance_file), + file(testDataSetup.expression_test_data_dir + testDataSetup.abundance_file), 'deseq2', // analysis method 1.5, // FC threshold 0.05 // padj threshold @@ -210,7 +210,7 @@ nextflow_workflow { // get input from upstream subworkflow ch_input = ABUNDANCE_DIFFERENTIAL_FILTER.out.normalised_matrix - .combine(Channel.fromPath(testData.genesets_file)) + .combine(channel.fromPath(testData.genesets_file)) .map { meta, matrix, genesets -> [meta, matrix, genesets, [], 'gsea'] } @@ -219,7 +219,7 @@ nextflow_workflow { ch_contrasts = ch_input .map {it[0]} .combine( - Channel.fromPath(file(testData.contrasts_file)) + channel.fromPath(file(testData.contrasts_file)) .splitCsv ( header:true, sep:',' ) .map{ tuple(it, it.variable, it.reference, it.target, it.formula, it.comparison) @@ -228,11 +228,11 @@ nextflow_workflow { .groupTuple() ch_samplesheet = ch_input .map {it[0]} - .combine( Channel.of(file(testData.samplesheet_file)) ) + .combine( channel.of(file(testData.samplesheet_file)) ) ch_featuresheet = ch_input .map {it[0]} .combine( - Channel.of([ + channel.of([ file(testData.abundance_file), 'gene_id', 'gene_name' @@ -269,7 +269,7 @@ nextflow_workflow { workflow { """ // Define test data - def testData = [ + def testDataSetup = [ expression_test_data_dir: params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/', contrasts_file: 'SRP254919.contrasts.csv', abundance_file: 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', @@ -277,21 +277,21 @@ nextflow_workflow { ] // Define inputs - ch_samplesheet = Channel.of([ + ch_samplesheet = channel.of([ [ id:'test' ], - file(testData.expression_test_data_dir + testData.samplesheet_file) + file(testDataSetup.expression_test_data_dir + testDataSetup.samplesheet_file) ]) - ch_transcript_lengths = Channel.of([ [], [] ]) - ch_control_features = Channel.of([ [], [] ]) - ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file)) + ch_transcript_lengths = channel.of([ [], [] ]) + ch_control_features = channel.of([ [], [] ]) + ch_contrasts = channel.fromPath(file(testDataSetup.expression_test_data_dir + testDataSetup.contrasts_file)) .splitCsv ( header:true, sep:',' ) .map{ tuple([ id:'test' ], it, it.variable, it.reference, it.target, it.formula, it.comparison) } .groupTuple() - ch_input = Channel.of([ + ch_input = channel.of([ [ id:'test' ], - file(testData.expression_test_data_dir + testData.abundance_file), + file(testDataSetup.expression_test_data_dir + testDataSetup.abundance_file), 'propd', // analysis method 1.5, // FC threshold 0.05 // significance threshold (automatically given by propd, not necessary) @@ -311,7 +311,7 @@ nextflow_workflow { workflow { """ ch_input = ABUNDANCE_DIFFERENTIAL_FILTER.out.adjacency - .combine(Channel.fromPath(params.modules_testdata_base_path + 'genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt')) + .combine(channel.fromPath(params.modules_testdata_base_path + 'genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt')) .map { meta, results, genesets -> [meta, results, genesets, [], 'grea'] } @@ -320,8 +320,8 @@ nextflow_workflow { [meta, [], '', ''] } input[0] = ch_input - input[1] = Channel.of([[], [], [], [], [], []]) - input[2] = Channel.of([[], []]) + input[1] = channel.of([[], [], [], [], [], []]) + input[2] = channel.of([[], []]) input[3] = ch_featuresheet """ } @@ -349,7 +349,7 @@ nextflow_workflow { workflow { """ // Define test data - def testData = [ + def testDataSetup = [ expression_test_data_dir: params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/', contrasts_file: 'SRP254919.contrasts.csv', abundance_file: 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', @@ -357,36 +357,36 @@ nextflow_workflow { ] // Define inputs - ch_samplesheet = Channel.of([ + ch_samplesheet = channel.of([ [ id:'test' ], - file(testData.expression_test_data_dir + testData.samplesheet_file) + file(testDataSetup.expression_test_data_dir + testDataSetup.samplesheet_file) ]) - ch_transcript_lengths = Channel.of([ [], [] ]) - ch_control_features = Channel.of([ [], [] ]) - ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file)) + ch_transcript_lengths = channel.of([ [], [] ]) + ch_control_features = channel.of([ [], [] ]) + ch_contrasts = channel.fromPath(file(testDataSetup.expression_test_data_dir + testDataSetup.contrasts_file)) .splitCsv ( header:true, sep:',' ) .map{ tuple([ id:'test' ], it, it.variable, it.reference, it.target, it.formula, it.comparison) } .groupTuple() - ch_input = Channel.of( + ch_input = channel.of( [ [ id:'test' ], - file(testData.expression_test_data_dir + testData.abundance_file), + file(testDataSetup.expression_test_data_dir + testDataSetup.abundance_file), 'deseq2', 1.5, // FC threshold 0.05 // stat (adjusted p-value) threshold ], [ [ id:'test' ], - file(testData.expression_test_data_dir + testData.abundance_file), + file(testDataSetup.expression_test_data_dir + testDataSetup.abundance_file), 'limma', 1.5, // FC threshold 0.05 // stat (adjusted p-value) threshold ], [ [ id:'test' ], - file(testData.expression_test_data_dir + testData.abundance_file), + file(testDataSetup.expression_test_data_dir + testDataSetup.abundance_file), 'propd', 1.5, // FC threshold 0.05 // significance threshold (automatically given by propd, not necessary) @@ -417,15 +417,15 @@ nextflow_workflow { // define input channels ch_input_for_gprofiler2 = ABUNDANCE_DIFFERENTIAL_FILTER.out.results_genewise_filtered - .combine(Channel.of('gprofiler2')) + .combine(channel.of('gprofiler2')) ch_input_for_gsea = ABUNDANCE_DIFFERENTIAL_FILTER.out.normalised_matrix - .combine(Channel.of('gsea')) + .combine(channel.of('gsea')) ch_input_for_grea = ABUNDANCE_DIFFERENTIAL_FILTER.out.adjacency - .combine(Channel.of('grea')) + .combine(channel.of('grea')) ch_input = ch_input_for_gprofiler2 .mix(ch_input_for_gsea) .mix(ch_input_for_grea) - .combine(Channel.fromPath(testData.genesets_file)) + .combine(channel.fromPath(testData.genesets_file)) .map { meta, input_file, method, genesets -> [meta, input_file, genesets, [], method] } @@ -434,7 +434,7 @@ nextflow_workflow { ch_contrasts = ch_input .map {it[0]} .combine( - Channel.fromPath(file(testData.contrasts_file)) + channel.fromPath(file(testData.contrasts_file)) .splitCsv ( header:true, sep:',' ) .map{ tuple(it, it.variable, it.reference, it.target, it.formula, it.comparison) @@ -443,11 +443,11 @@ nextflow_workflow { .groupTuple() ch_samplesheet = ch_input .map {it[0]} - .combine( Channel.of(file(testData.samplesheet_file)) ) + .combine( channel.of(file(testData.samplesheet_file)) ) ch_featuresheet = ch_input .map {it[0]} .combine( - Channel.of([ + channel.of([ file(testData.abundance_file), 'gene_id', 'gene_name' @@ -486,7 +486,7 @@ nextflow_workflow { when { workflow { """ - ch_input = Channel.of([ + ch_input = channel.of([ [ 'id':'treatment_mCherry_hND6', 'method_differential':'deseq2', @@ -500,9 +500,9 @@ nextflow_workflow { 'decoupler' ]) - ch_contrasts = Channel.of([[], [], [], [], [], []]) - ch_samplesheet = Channel.of([[], []]) - ch_featuresheet = Channel.of([ + ch_contrasts = channel.of([[], [], [], [], [], []]) + ch_samplesheet = channel.of([[], []]) + ch_featuresheet = channel.of([ [ 'id':'treatment_mCherry_hND6', 'method_differential':'deseq2', @@ -553,7 +553,7 @@ nextflow_workflow { when { workflow { """ - ch_input = Channel.of([ + ch_input = channel.of([ ['id':'Condition_genotype_WT_KO', 'variable':'Condition genotype', 'reference':'WT', 'target':'KO', 'blocking':'batch'], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/Condition_genotype_WT_KO.deseq2.results_filtered.tsv", checkIfExists: true), [], @@ -562,9 +562,9 @@ nextflow_workflow { ]) input[0] = ch_input - input[1] = Channel.of([[], [], [], [], [], []]) - input[2] = Channel.of([[], []]) - input[3] = Channel.of([ + input[1] = channel.of([[], [], [], [], [], []]) + input[2] = channel.of([[], []]) + input[3] = channel.of([ ['id':'Condition_genotype_WT_KO', 'variable':'Condition genotype', 'reference':'WT', 'target':'KO', 'blocking':'batch'], [], '',