diff --git a/CHANGELOG.md b/CHANGELOG.md index fa465e78..588bc318 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ Special thanks to the following for their contributions to the release: - [Alexander Blaessle](https://github.com/alexblaessle) - [Lukas Forer](https://github.com/lukfor) - [Maxime Garcia](https://github.com/maxulysse) +- [Sateesh Peri](https://github.com/sateeshperi) - [Sebastian Uhrig](https://github.com/suhrig) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. @@ -52,6 +53,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #290](https://github.com/nf-core/fetchngs/pull/290) - Remove mentions of deprecated Synapse functionality in pipeline - [PR #294](https://github.com/nf-core/fetchngs/pull/294) - Replace mermaid diagram with subway map - [PR #295](https://github.com/nf-core/fetchngs/pull/295) - Be less stringent with test expectations for CI +- [PR #296](https://github.com/nf-core/fetchngs/pull/296) - Remove params.outdir from tests where required and update snapshots ### Software dependencies diff --git a/modules.json b/modules.json index 71a3e25c..93f4553b 100644 --- a/modules.json +++ b/modules.json @@ -7,23 +7,23 @@ "nf-core": { "custom/sratoolsncbisettings": { "branch": "master", - "git_sha": "3aa09ac8899d7735cb5bc004da0ef5f35f9a7901", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "sratools/fasterqdump": { "branch": "master", - "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"], "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff" }, "sratools/prefetch": { "branch": "master", - "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "untar": { "branch": "master", - "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["modules"] } } @@ -32,22 +32,22 @@ "nf-core": { "fastq_download_prefetch_fasterqdump_sratools": { "branch": "master", - "git_sha": "3aa09ac8899d7735cb5bc004da0ef5f35f9a7901", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] } } diff --git a/modules/local/aspera_cli/tests/main.nf.test b/modules/local/aspera_cli/tests/main.nf.test index b2f5f1bd..63347000 100644 --- a/modules/local/aspera_cli/tests/main.nf.test +++ b/modules/local/aspera_cli/tests/main.nf.test @@ -7,10 +7,6 @@ nextflow_process { test("Should run without failures") { when { - params { - outdir = "$outputDir" - } - process { """ input[0] = [ diff --git a/modules/local/aspera_cli/tests/main.nf.test.snap b/modules/local/aspera_cli/tests/main.nf.test.snap index 15497822..0ba6a643 100644 --- a/modules/local/aspera_cli/tests/main.nf.test.snap +++ b/modules/local/aspera_cli/tests/main.nf.test.snap @@ -66,6 +66,10 @@ ] } ], - "timestamp": "2024-01-29T13:00:29.847293" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:52:00.601018" } } \ No newline at end of file diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test index 106f3248..dbb4d74f 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -7,10 +7,6 @@ nextflow_process { test("Should run without failures") { when { - params { - outdir = "$outputDir" - } - process { """ input[0] = file(params.pipelines_testdata_base_path + 'csv/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true) diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap index 1a4d16c4..43e46f61 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap @@ -22,6 +22,10 @@ ] } ], - "timestamp": "2023-09-22T10:58:18.132284" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:52:12.65888" } } \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test index f58aaae2..bf005290 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -7,10 +7,6 @@ nextflow_process { test("Should run without failures") { when { - params { - outdir = "$outputDir" - } - process { """ input[0] = [ diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap index 531a5ec3..5b300f8c 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap @@ -66,6 +66,10 @@ ] } ], - "timestamp": "2023-12-20T23:33:35.159073" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:51:51.301654" } } \ No newline at end of file diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test index 2e510ea1..48797a1a 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -7,10 +7,6 @@ nextflow_process { test("Should run without failures") { when { - params { - outdir = "$outputDir" - } - process { """ input[0] = 'SRR13191702' diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap index 241efe2a..f7b6cee5 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap @@ -16,6 +16,10 @@ ] } ], - "timestamp": "2023-09-22T10:58:56.721948" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:52:05.345153" } } \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test index 4b03249c..39db814a 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -7,10 +7,6 @@ nextflow_process { test("Should run without failures") { when { - params { - outdir = "$outputDir" - } - process { """ input[0] = file(params.pipelines_testdata_base_path + 'tsv/SRR13191702.runinfo.tsv', checkIfExists: true) diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap index cd246303..be190f5a 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap @@ -16,6 +16,10 @@ ] } ], - "timestamp": "2023-09-22T10:58:36.16611" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:51:45.748227" } } \ No newline at end of file diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test index 4458858e..ed765158 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -7,10 +7,6 @@ nextflow_process { test("Should run without failures") { when { - params { - outdir = "$outputDir" - } - process { """ input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867', experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7', sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false] diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap index 8cc8686a..568f3ea7 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap @@ -108,6 +108,10 @@ ] } ], - "timestamp": "2023-09-22T10:58:27.169349" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:51:38.244046" } } \ No newline at end of file diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test index 8cd0de8a..e9ea68dc 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test @@ -11,7 +11,6 @@ nextflow_process { params { settings_path = '/tmp/.ncbi' settings_file = "${params.settings_path}/user-settings.mkfg" - outdir = "$outputDir" } process { diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap index 65a706d4..5e314f0b 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap @@ -5,6 +5,10 @@ "versions.yml:md5,3d6ee88cce1ee517e198633f062589a8" ] ], - "timestamp": "2024-01-09T22:43:44.996003" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:47:15.824443" } -} +} \ No newline at end of file diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config index c4a96e94..df5def04 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config @@ -4,8 +4,6 @@ params.settings_file = "${params.settings_path}/user-settings.mkfg" env.NCBI_SETTINGS = params.settings_file process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: CUSTOM_SRATOOLSNCBISETTINGS { containerOptions = { (workflow.containerEngine == 'singularity') ? diff --git a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff index 1fb8cbf4..089862bf 100644 --- a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff +++ b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff @@ -38,7 +38,7 @@ Changes in module 'nf-core/sratools/fasterqdump' --- modules/nf-core/sratools/fasterqdump/tests/main.nf.test +++ modules/nf-core/sratools/fasterqdump/tests/main.nf.test -@@ -3,11 +3,9 @@ +@@ -3,11 +3,8 @@ script "../main.nf" config "./nextflow.config" process "SRATOOLS_FASTERQDUMP" @@ -47,7 +47,6 @@ Changes in module 'nf-core/sratools/fasterqdump' - tag "untar" - tag "sratools" - tag "sratools/fasterqdump" -+ tag "SRATOOLS_FASTERQDUMP" + + tag "UNTAR" diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test index c64f6fc1..695394d4 100644 --- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test @@ -20,10 +20,6 @@ nextflow_process { } when { - params { - outdir = "$outputDir" - } - process { """ input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]} @@ -55,10 +51,6 @@ nextflow_process { } when { - params { - outdir = "$outputDir" - } - process { """ input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]} diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap index 0e590311..ce0f9800 100644 --- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap @@ -28,7 +28,11 @@ ] } ], - "timestamp": "2024-01-30T18:02:53.958171" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-28T15:25:52.837288" }, "Paired-end": { "content": [ @@ -65,6 +69,10 @@ ] } ], - "timestamp": "2024-01-30T18:03:20.841426" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-28T15:26:42.466223" } } \ No newline at end of file diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test index b0f5ffa2..c3ebd91e 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test @@ -6,9 +6,6 @@ nextflow_process { test("sratools/prefetch") { when { - params { - outdir = "output" - } process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ]) @@ -29,9 +26,6 @@ nextflow_process { test("sratools/prefetch with sralite") { when { - params { - outdir = "output" - } process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], 'SRR1170046' ]) diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap index ab1d2088..946fc869 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap @@ -32,7 +32,11 @@ ] } ], - "timestamp": "2023-10-13T12:11:24.563510389" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:49:02.309737" }, "sratools/prefetch": { "content": [ @@ -67,6 +71,10 @@ ] } ], - "timestamp": "2023-10-13T12:11:02.75256571" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:48:37.428307" } } \ No newline at end of file diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index 05134043..98b769ad 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -7,9 +7,6 @@ nextflow_process { test("test_untar") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] @@ -29,9 +26,6 @@ nextflow_process { test("test_untar_onlyfiles") { when { - params { - outdir = "$outputDir" - } process { """ 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 ace42576..64550292 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -12,7 +12,11 @@ ] ] ], - "timestamp": "2023-10-18T11:56:46.878844" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:49:41.320643" }, "test_untar": { "content": [ @@ -29,6 +33,10 @@ ] ] ], - "timestamp": "2023-10-18T11:56:08.16574" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:49:33.795172" } } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test index 85c16bf9..f2e3f12a 100644 --- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test +++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test @@ -69,8 +69,10 @@ nextflow_function { function "sraCurateSamplesheetWarn" then { - assert function.success - assert snapshot(function.result).match() + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) } } diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap index 05840fc8..99fb20e7 100644 --- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap @@ -1,16 +1,28 @@ { "Function sraCurateSamplesheetWarn": { "content": null, - "timestamp": "2024-01-19T16:37:05.668505" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:55:41.001798" }, "Function sraCheckENAMetadataFields [success]": { "content": null, - "timestamp": "2024-01-19T16:36:51.121603" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:55:33.679255" }, "Function isSraId": { "content": [ true ], - "timestamp": "2024-01-19T16:36:43.68958" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T11:55:29.999289" } } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test index b2114675..b94f72cf 100644 --- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test +++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test @@ -8,15 +8,12 @@ nextflow_workflow { test("Should run") { when { - params { - outdir = "tests/results" - } workflow { """ email = null email_on_fail = null plaintext_email = false - outdir = "tests/results" + outdir = 'results' monochrome_logs = false hook_url = null diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test index 377d91f2..e04aa726 100644 --- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test +++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test @@ -8,9 +8,6 @@ nextflow_workflow { test("Should run") { when { - params { - outdir = "tests/results" - } workflow { """ version = false @@ -18,7 +15,7 @@ nextflow_workflow { validate_params = false monochrome_logs = false nextflow_cli_args = [] - outdir = "$params.outdir" + outdir = 'results' ena_metadata_fields = null input[0] = version diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test index 7293a792..7b41ed7e 100644 --- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test @@ -20,9 +20,6 @@ nextflow_workflow { input[1] = [] """ } - params { - outdir = "output" - } } then { diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap index d64857ef..485411da 100644 --- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap @@ -7,7 +7,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-01T08:34:54.56022" + "timestamp": "2024-02-28T12:02:56.176292" }, "test_pe_reads_2_lines": { "content": [ @@ -24,7 +24,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-01T08:34:54.532626" + "timestamp": "2024-02-28T12:02:56.166207" }, "test_pe_reads_2_size": { "content": [ @@ -34,7 +34,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-01T08:34:54.542804" + "timestamp": "2024-02-28T12:02:56.168869" }, "versions": { "content": [ @@ -46,9 +46,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.01.0" }, - "timestamp": "2024-02-01T08:34:54.570734" + "timestamp": "2024-02-28T15:19:18.755939" }, "test_pe_reads_1_size": { "content": [ @@ -56,9 +56,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.01.0" }, - "timestamp": "2024-02-01T08:34:54.525795" + "timestamp": "2024-02-28T15:19:18.677234" }, "test_se_reads_lines": { "content": [ @@ -75,7 +75,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-01T08:34:54.550392" + "timestamp": "2024-02-28T12:02:56.171227" }, "test_pe_reads_1_lines": { "content": [ @@ -92,6 +92,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-01T08:34:54.509486" + "timestamp": "2024-02-28T12:02:56.161354" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap index db2030f8..e3f0baf4 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -3,10 +3,18 @@ "content": [ "v9.9.9" ], - "timestamp": "2024-01-19T11:32:36.031083" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" }, "Test Function checkCondaChannels": { "content": null, - "timestamp": "2024-01-19T11:32:50.456" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index 94e7198c..13782037 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -8,9 +8,6 @@ nextflow_workflow { test("Should run no inputs") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = false @@ -36,9 +33,6 @@ nextflow_workflow { test("Should print version") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = true @@ -65,19 +59,16 @@ nextflow_workflow { test("Should dump params") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = 'results' check_conda_channels = false input[0] = false input[1] = true - input[2] = params.outdir + input[2] = outdir input[3] = false """ } @@ -93,19 +84,16 @@ nextflow_workflow { test("Should not create params JSON if no output directory") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = null check_conda_channels = false input[0] = false input[1] = true - input[2] = null + input[2] = outdir input[3] = false """ } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 10f948e6..1037232c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -1,25 +1,41 @@ { "Test Function checkProfileProvided": { "content": null, - "timestamp": "2024-02-09T15:43:55.145717" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" }, "Test Function checkConfigProvided": { "content": [ true ], - "timestamp": "2024-01-19T11:34:13.548431224" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:59.729647" }, "Test Function nfCoreLogo": { "content": [ "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" ], - "timestamp": "2024-01-19T11:34:38.840454873" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:10.562934" }, "Test Function workflowCitation": { "content": [ "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" ], - "timestamp": "2024-01-19T11:34:22.24352016" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:07.019761" }, "Test Function without logColours": { "content": [ @@ -73,13 +89,21 @@ "biwhite": "" } ], - "timestamp": "2024-01-19T11:35:04.418416984" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" }, "Test Function dashedLine": { "content": [ "-\u001b[2m----------------------------------------------------\u001b[0m-" ], - "timestamp": "2024-01-19T11:34:55.420000755" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:14.366181" }, "Test Function with logColours": { "content": [ @@ -133,6 +157,10 @@ "biwhite": "\u001b[1;97m" } ], - "timestamp": "2024-01-19T11:35:13.436366565" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap index d07ce54c..859d1030 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -10,6 +10,10 @@ ] } ], - "timestamp": "2024-01-19T11:35:22.538940073" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" } } \ No newline at end of file diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index dddc5275..1e2856c1 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -20,9 +20,6 @@ nextflow_workflow { input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - outdir = "$outputDir" - } } then { diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 98d1432d..c8d17876 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -21,7 +21,6 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" nf_core_pipeline = "rnaseq" ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" sample_mapping_fields = "run_accession,library_layout" diff --git a/workflows/sra/tests/sra_download_method_aspera.nf.test b/workflows/sra/tests/sra_download_method_aspera.nf.test index d36f9095..d431a571 100644 --- a/workflows/sra/tests/sra_download_method_aspera.nf.test +++ b/workflows/sra/tests/sra_download_method_aspera.nf.test @@ -21,7 +21,6 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" download_method = 'aspera' } } diff --git a/workflows/sra/tests/sra_download_method_sratools.nf.test b/workflows/sra/tests/sra_download_method_sratools.nf.test index 05613f1e..e4f8c2d2 100644 --- a/workflows/sra/tests/sra_download_method_sratools.nf.test +++ b/workflows/sra/tests/sra_download_method_sratools.nf.test @@ -21,7 +21,6 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" download_method = 'sratools' } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 522ab75b..72f8d595 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -21,7 +21,6 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" nf_core_pipeline = "atacseq" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index f6f1b560..2e20902a 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -21,7 +21,6 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" nf_core_pipeline = "rnaseq" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index b9373b57..50650b79 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -21,7 +21,6 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" nf_core_pipeline = "taxprofiler" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 4985b9d0..1fe9cc41 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -21,7 +21,6 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" nf_core_pipeline = "viralrecon" } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 245dbb80..8663cf3f 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -20,7 +20,6 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" skip_fastq_download = true } }