diff --git a/CHANGELOG.md b/CHANGELOG.md index cff689f5fa..039b93d0c0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1408](https://github.com/nf-core/sarek/pull/1408), [#1412](https://github.com/nf-core/sarek/pull/1412) - Updating samtools to v1.19.2 - except in GATK/markduplicates. (Temporarily disabled nf-test for bwamem2/mem.) - [#1411](https://github.com/nf-core/sarek/pull/1411) - Temporarily disable sentieon related tests - [#1419](https://github.com/nf-core/sarek/pull/1419) - Updating GATK to v4.5, and updating samtools to v1.19.2 in GATK/markduplicates. +- [#1426](https://github.com/nf-core/sarek/pull/1426) - Updating certain modules in order to fix the testdata-path in the nf-tests of those modules. Setting Docker runOptions for params.use_gatk_spark. - [#1428](https://github.com/nf-core/sarek/pull/1428) - Sync `TEMPLATE` with `tools` `2.13.1` ### Fixed diff --git a/conf/test.config b/conf/test.config index 28bd2f7bf3..002b35d183 100644 --- a/conf/test.config +++ b/conf/test.config @@ -108,6 +108,7 @@ if (System.getenv('PROFILE')) { } else if ("$PROFILE" == "docker") { conda.enabled = false docker.enabled = true + docker.runOptions = { params.use_gatk_spark ? '' : '-u $(id -u):$(id -g)' }.call() charliecloud.enabled = false podman.enabled = false shifter.enabled = false diff --git a/conf/test/cache.config b/conf/test/cache.config index f6d0ceca79..5aba7dc0f6 100644 --- a/conf/test/cache.config +++ b/conf/test/cache.config @@ -116,6 +116,7 @@ if (System.getenv('PROFILE')) { } else if ("$PROFILE" == "docker") { conda.enabled = false docker.enabled = true + docker.runOptions = { params.use_gatk_spark ? '' : '-u $(id -u):$(id -g)' }.call() charliecloud.enabled = false podman.enabled = false shifter.enabled = false diff --git a/conf/test/use_gatk_spark.config b/conf/test/use_gatk_spark.config index bd40af1b77..41bbc16452 100644 --- a/conf/test/use_gatk_spark.config +++ b/conf/test/use_gatk_spark.config @@ -14,3 +14,5 @@ params { use_gatk_spark = 'baserecalibrator,markduplicates' input = "${projectDir}/tests/csv/3.0/fastq_tumor_only.csv" } + +docker.runOptions = '' diff --git a/modules.json b/modules.json index bf2e991807..bdd0e0a720 100644 --- a/modules.json +++ b/modules.json @@ -38,12 +38,12 @@ }, "bwa/index": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "6278bf9afd4a4b2d00fa6052250e73da3d91546f", "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", - "git_sha": "ba3f3df395d2719dcef5c67189042a1dc555c701", + "git_sha": "5908e575322666ccc33911a28b06e3f82260fe54", "installed_by": ["modules"] }, "bwamem2/index": { @@ -58,12 +58,12 @@ }, "cat/cat": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "0997b47c93c06b49aa7b3fefda87e728312cf2ca", "installed_by": ["modules"] }, "cnvkit/antitarget": { @@ -119,7 +119,7 @@ }, "dragmap/align": { "branch": "master", - "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", + "git_sha": "9a7efcec9b21baf1c67342faa6b8d905c972207f", "installed_by": ["modules"], "patch": "modules/nf-core/dragmap/align/dragmap-align.diff" }, @@ -171,7 +171,7 @@ }, "gatk4/applybqsr": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "af273ea6618c50e82c372abe18b0a225e84fe6f7", "installed_by": ["modules"] }, "gatk4/applyvqsr": { @@ -181,7 +181,7 @@ }, "gatk4/baserecalibrator": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "8a223e11d4e6deb36484e01891eae9c1cacb5f5d", "installed_by": ["modules"] }, "gatk4/calculatecontamination": { @@ -226,7 +226,7 @@ }, "gatk4/genomicsdbimport": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "194fca815cf594646e638fa5476acbcc296f1850", "installed_by": ["modules"] }, "gatk4/genotypegvcfs": { @@ -256,7 +256,7 @@ }, "gatk4/markduplicates": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "194fca815cf594646e638fa5476acbcc296f1850", "installed_by": ["modules"] }, "gatk4/mergemutectstats": { @@ -266,7 +266,7 @@ }, "gatk4/mergevcfs": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "194fca815cf594646e638fa5476acbcc296f1850", "installed_by": ["modules"] }, "gatk4/mutect2": { @@ -466,7 +466,7 @@ }, "untar": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620", "installed_by": ["modules"] }, "unzip": { diff --git a/modules/nf-core/bwa/index/tests/main.nf.test b/modules/nf-core/bwa/index/tests/main.nf.test index 5fc8d49662..af33e73ca1 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test +++ b/modules/nf-core/bwa/index/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_process { """ input[0] = [ [id: 'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -29,5 +29,5 @@ nextflow_process { } } - + } diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test b/modules/nf-core/bwa/mem/tests/main.nf.test index cd6591ff27..2696e4bfe9 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test +++ b/modules/nf-core/bwa/mem/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { """ input[0] = [ [id: 'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -31,7 +31,7 @@ nextflow_process { input[0] = [ [ id:'test', single_end:true ], // meta map [ - 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] = BWA_INDEX.out.index @@ -58,7 +58,7 @@ nextflow_process { """ input[0] = [ [id: 'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -71,7 +71,7 @@ nextflow_process { input[0] = [ [ id:'test', single_end:true ], // meta map [ - 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] = BWA_INDEX.out.index @@ -98,7 +98,7 @@ nextflow_process { """ input[0] = [ [id: 'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -111,8 +111,8 @@ 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) ] ] input[1] = BWA_INDEX.out.index @@ -139,7 +139,7 @@ nextflow_process { """ input[0] = [ [id: 'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -152,8 +152,8 @@ 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) ] ] input[1] = BWA_INDEX.out.index diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 4264a92ccc..adbdbd7ba6 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -22,6 +22,8 @@ process CAT_CAT { def args2 = task.ext.args2 ?: '' def file_list = files_in.collect { it.toString() } + // choose appropriate concatenation tool depending on input and output format + // | input | output | command1 | command2 | // |-----------|------------|----------|----------| // | gzipped | gzipped | cat | | @@ -30,11 +32,15 @@ process CAT_CAT { // | ungzipped | gzipped | cat | pigz | // Use input file ending as default - prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" + prefix = task.ext.prefix ?: "${meta.id}${getFileSuffix(file_list[0])}" out_zip = prefix.endsWith('.gz') in_zip = file_list[0].endsWith('.gz') command1 = (in_zip && !out_zip) ? 'zcat' : 'cat' command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : '' + if(file_list.contains(prefix.trim())) { + error "The name of the input file can't be the same as for the output prefix in the " + + "module CAT_CAT (currently `$prefix`). Please choose a different one." + } """ $command1 \\ $args \\ @@ -49,8 +55,12 @@ process CAT_CAT { """ stub: - def file_list = files_in.collect { it.toString() } - prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" + def file_list = files_in.collect { it.toString() } + prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" + if(file_list.contains(prefix.trim())) { + error "The name of the input file can't be the same as for the output prefix in the " + + "module CAT_CAT (currently `$prefix`). Please choose a different one." + } """ touch $prefix @@ -60,3 +70,10 @@ process CAT_CAT { END_VERSIONS """ } + +// for .gz files also include the second to last extension if it is present. E.g., .fasta.gz +def getFileSuffix(filename) { + def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/ + return match ? match[0][1] : filename.substring(filename.lastIndexOf('.')) +} + diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test index 5766daafbe..fcee2d19f2 100644 --- a/modules/nf-core/cat/cat/tests/main.nf.test +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -8,6 +8,32 @@ nextflow_process { tag "cat" tag "cat/cat" + test("test_cat_name_conflict") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'genome', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert !process.success }, + { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") } + ) + } + } + test("test_cat_unzipped_unzipped") { when { params { @@ -19,8 +45,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) ] ] """ @@ -46,8 +72,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) ] ] """ @@ -76,8 +102,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) ] ] """ @@ -105,8 +131,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) ] ] """ @@ -134,7 +160,7 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] ] """ @@ -150,4 +176,3 @@ nextflow_process { } } } - diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index bff93add01..8c69b121f7 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::sed=4.7 + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 3d963784cb..f132b2adc1 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -76,5 +76,4 @@ process CAT_FASTQ { """ } } - } diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test index f5f941825c..dab2e14c02 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -16,11 +16,11 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ 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)] + ]) """ } } @@ -28,8 +28,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -42,13 +41,13 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ 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.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_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), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -56,8 +55,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -70,11 +68,11 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: 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), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -82,8 +80,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -96,13 +93,13 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ 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.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), + 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)] + ]) """ } } @@ -110,8 +107,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -124,10 +120,10 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ 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)] + ]) """ } } @@ -135,8 +131,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap index ec2342e549..43dfe28fc7 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -1,78 +1,169 @@ { "test_cat_fastq_single_end": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,f9cf5e375f7de81a406144a2c70cc64d" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2023-10-17T23:19:12.990284837" + "timestamp": "2024-01-17T17:30:39.816981" }, "test_cat_fastq_single_end_same_name": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,63f817db7a29a03eb538104495556f66" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2023-10-17T23:19:31.554568147" + "timestamp": "2024-01-17T17:32:35.229332" }, "test_cat_fastq_single_end_single_file": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,e325ef7deb4023447a1f074e285761af" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2023-10-17T23:19:49.629360033" + "timestamp": "2024-01-17T17:34:00.058829" }, "test_cat_fastq_paired_end_same_name": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, + { + "0": [ [ - "test_1.merged.fastq.gz:md5,63f817db7a29a03eb538104495556f66", - "test_2.merged.fastq.gz:md5,fe9f266f43a6fc3dcab690a18419a56e" + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2023-10-17T23:19:40.711617539" + "timestamp": "2024-01-17T17:33:33.031555" }, "test_cat_fastq_paired_end": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ [ - "test_1.merged.fastq.gz:md5,f9cf5e375f7de81a406144a2c70cc64d", - "test_2.merged.fastq.gz:md5,77c8e966e130d8c6b6ec9be52fcb2bda" + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2023-10-18T07:53:20.923560211" + "timestamp": "2024-01-17T17:32:02.270935" } } \ No newline at end of file diff --git a/modules/nf-core/dragmap/align/tests/main.nf.test b/modules/nf-core/dragmap/align/tests/main.nf.test index c90c78f314..ab6a8d1d26 100644 --- a/modules/nf-core/dragmap/align/tests/main.nf.test +++ b/modules/nf-core/dragmap/align/tests/main.nf.test @@ -7,6 +7,7 @@ nextflow_process { tag "modules_nfcore" tag "dragmap" tag "dragmap/align" + tag "dragmap/hashtable" test("sarscov2 - fastq, hashtable, false") { @@ -17,7 +18,7 @@ nextflow_process { """ input[0] = [ [id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -29,7 +30,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - 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] = DRAGMAP_HASHTABLE.out.hashmap input[2] = false //sort @@ -59,7 +60,7 @@ nextflow_process { """ input[0] = [ [id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -71,7 +72,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - 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] = DRAGMAP_HASHTABLE.out.hashmap input[2] = true //sort @@ -101,7 +102,7 @@ nextflow_process { """ input[0] = [ [id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -114,8 +115,8 @@ 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) ] ] input[1] = DRAGMAP_HASHTABLE.out.hashmap @@ -146,7 +147,7 @@ nextflow_process { """ input[0] = [ [id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -159,8 +160,8 @@ 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) ] ] input[1] = DRAGMAP_HASHTABLE.out.hashmap @@ -191,7 +192,7 @@ nextflow_process { """ input[0] = [ [id:'test'], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ } @@ -204,8 +205,8 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ] input[1] = DRAGMAP_HASHTABLE.out.hashmap @@ -237,7 +238,7 @@ nextflow_process { """ input[0] = [ [id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -250,8 +251,8 @@ 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) ] ] input[1] = DRAGMAP_HASHTABLE.out.hashmap diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test index 5ee53d5cb5..3d9c6204f7 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test @@ -16,14 +16,14 @@ nextflow_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']['illumina']['test_baserecalibrator_table'], 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/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', 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) """ } } @@ -44,14 +44,14 @@ nextflow_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']['illumina']['test_baserecalibrator_table'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], 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/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true), + 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) """ } } @@ -71,14 +71,14 @@ nextflow_process { """ input[0] = [ [ 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), - file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], 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/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/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[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) """ } } diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test index 1262b69441..fbd91beae2 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test @@ -15,15 +15,15 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - 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.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] = 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[4] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) - input[5] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], 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] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) """ } @@ -45,15 +45,15 @@ nextflow_process { input[0] = [ [ id:'test' ], // meta map - 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) + 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] = 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[4] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) - input[5] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], 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] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) """ } @@ -75,20 +75,20 @@ nextflow_process { input[0] = [ [ id:'test' ], // meta map - 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.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] = 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] = [ - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], 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/test2.vcf.gz', checkIfExists: true) ] input[5] = [ - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] """ @@ -141,15 +141,15 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - 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), + 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] = 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[4] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) - input[5] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_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] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test index 0902621643..9c207b3074 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test +++ b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test @@ -17,9 +17,9 @@ nextflow_process { """ // [meta, vcf, tbi, interval, interval_value, workspace ] input[0] = [ [ id:'test'], - 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_interval_list'], checkIfExists: true) , + 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.interval_list', checkIfExists: true) , [] , [] ] // run_intlist @@ -51,7 +51,7 @@ nextflow_process { script "../../../untar/main.nf" process { """ - input[0] = Channel.of([ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]) + input[0] = Channel.of([ [], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz', checkIfExists: true) ]) """ } } @@ -89,7 +89,7 @@ nextflow_process { script "../../../untar/main.nf" process { """ - input[0] = Channel.of([ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]) + input[0] = Channel.of([ [], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz', checkIfExists: true) ]) """ } } @@ -98,7 +98,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ [id:"test"], file( params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'] , checkIfExists: true), file( params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz_tbi'] , checkIfExists: true), [], []]).combine(UNTAR.out.untar.map{ it[1] }) + input[0] = Channel.of([ [id:"test"], file( params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz' , checkIfExists: true), file( params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi' , checkIfExists: true), [], []]).combine(UNTAR.out.untar.map{ it[1] }) // run_intlist input[1] = false // run_updatewspace @@ -129,9 +129,9 @@ nextflow_process { """ // [meta, vcf, tbi, interval, interval_value, workspace ] input[0] = [ [ id:'test'], - 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_interval_list'], checkIfExists: true) , + 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.interval_list', checkIfExists: true) , [] , [] ] // run_intlist diff --git a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test index d243b19ace..bbcf74db67 100644 --- a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test +++ b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] input[1] = [] input[2] = [] @@ -45,8 +45,8 @@ nextflow_process { input[0] = [ [ 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']['test2_paired_end_sorted_bam'], checkIfExists: true) + 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/test2.paired_end.sorted.bam', checkIfExists: true) ] ] input[1] = [] @@ -76,12 +76,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) + 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/test2.paired_end.sorted.bam', 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[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) """ } } diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test index e0237cfaed..77ace10a21 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test @@ -13,8 +13,8 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) ]] - input[1] = [ [], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)] + input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) ]] + input[1] = [ [], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)] """ } } @@ -37,7 +37,7 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) ]] + input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) ]] input[1] = [ [],[]] """ } @@ -64,7 +64,7 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) ]] + input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) ]] input[1] = [ [],[]] """ } diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index d6917da326..0c9cbb101d 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,9 +1,11 @@ name: untar + channels: - conda-forge - bioconda - defaults + dependencies: - - conda-forge::sed=4.7 - conda-forge::grep=3.11 + - conda-forge::sed=4.7 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index d40db13d82..679e83c784 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { } process { """ - input[0] = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ] + input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] """ } } @@ -30,28 +30,6 @@ nextflow_process { } - test("test_untar_different_output_path") { - - when { - params { - outdir = "$outputDir" - } - process { - """ - input[0] = [ [], file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) ] - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar_different_output_path") }, - ) - } - - } - test("test_untar_onlyfiles") { when { @@ -60,7 +38,7 @@ nextflow_process { } process { """ - input[0] = [ [], file(params.test_data['generic']['tar']['tar_gz'], checkIfExists: true) ] + input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] """ } } diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index 146c8678a7..ace4257668 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -1,483 +1,4 @@ { - 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docker.runOptions = '-u $(id -u):$(id -g)' + docker.runOptions = { params.use_gatk_spark ? '' : '-u $(id -u):$(id -g)' }.call() singularity.enabled = false } arm {