From 4572cb0ec0206de7ea6d2dc8104b86287f726c07 Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Tue, 5 May 2026 13:33:47 +0200 Subject: [PATCH 01/11] Added stub blocks to local modules --- modules/local/aspera_cli/main.nf | 15 +++++++++++++++ modules/local/multiqc_mappings_config/main.nf | 5 +++++ modules/local/sra_fastq_ftp/main.nf | 15 +++++++++++++++ modules/local/sra_ids_to_runinfo/main.nf | 5 +++++ modules/local/sra_runinfo_to_ftp/main.nf | 5 +++++ modules/local/sra_to_samplesheet/main.nf | 6 ++++++ 6 files changed, 51 insertions(+) diff --git a/modules/local/aspera_cli/main.nf b/modules/local/aspera_cli/main.nf index 41ae0565..1fbdf641 100644 --- a/modules/local/aspera_cli/main.nf +++ b/modules/local/aspera_cli/main.nf @@ -55,4 +55,19 @@ process ASPERA_CLI { md5sum -c ${meta.id}_2.fastq.gz.md5 """ } + + stub: + if (meta.single_end) { + """ + echo "" | gzip > ${meta.id}.fastq.gz + touch ${meta.id}.fastq.gz.md5 + """ + } else { + """ + echo "" | gzip > ${meta.id}_1.fastq.gz + echo "" | gzip > ${meta.id}_2.fastq.gz + touch ${meta.id}_1.fastq.gz.md5 + touch ${meta.id}_2.fastq.gz.md5 + """ + } } diff --git a/modules/local/multiqc_mappings_config/main.nf b/modules/local/multiqc_mappings_config/main.nf index deb3bb20..1691d410 100644 --- a/modules/local/multiqc_mappings_config/main.nf +++ b/modules/local/multiqc_mappings_config/main.nf @@ -19,4 +19,9 @@ process MULTIQC_MAPPINGS_CONFIG { $csv \\ multiqc_config.yml """ + + stub: + """ + touch multiqc_config.yml + """ } diff --git a/modules/local/sra_fastq_ftp/main.nf b/modules/local/sra_fastq_ftp/main.nf index 0770a161..79df44c7 100644 --- a/modules/local/sra_fastq_ftp/main.nf +++ b/modules/local/sra_fastq_ftp/main.nf @@ -48,4 +48,19 @@ process SRA_FASTQ_FTP { md5sum -c ${meta.id}_2.fastq.gz.md5 """ } + + stub: + if (meta.single_end) { + """ + echo "" | gzip > ${meta.id}.fastq.gz + touch ${meta.id}.fastq.gz.md5 + """ + } else { + """ + echo "" | gzip > ${meta.id}_1.fastq.gz + echo "" | gzip > ${meta.id}_2.fastq.gz + touch ${meta.id}_1.fastq.gz.md5 + touch ${meta.id}_2.fastq.gz.md5 + """ + } } diff --git a/modules/local/sra_ids_to_runinfo/main.nf b/modules/local/sra_ids_to_runinfo/main.nf index ff2e2da5..de5c3acc 100644 --- a/modules/local/sra_ids_to_runinfo/main.nf +++ b/modules/local/sra_ids_to_runinfo/main.nf @@ -25,4 +25,9 @@ process SRA_IDS_TO_RUNINFO { ${id}.runinfo.tsv \\ $metadata_fields """ + + stub: + """ + touch ${id}.runinfo.tsv + """ } diff --git a/modules/local/sra_runinfo_to_ftp/main.nf b/modules/local/sra_runinfo_to_ftp/main.nf index 49828c22..324ffa7b 100644 --- a/modules/local/sra_runinfo_to_ftp/main.nf +++ b/modules/local/sra_runinfo_to_ftp/main.nf @@ -19,4 +19,9 @@ process SRA_RUNINFO_TO_FTP { ${runinfo.join(',')} \\ ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv """ + + stub: + """ + touch ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv + """ } diff --git a/modules/local/sra_to_samplesheet/main.nf b/modules/local/sra_to_samplesheet/main.nf index 92edf5df..11b6f0d2 100644 --- a/modules/local/sra_to_samplesheet/main.nf +++ b/modules/local/sra_to_samplesheet/main.nf @@ -72,4 +72,10 @@ process SRA_TO_SAMPLESHEET { // Write mappings to file def mappings_file = task.workDir.resolve("${meta.id}.mappings.csv") mappings_file.text = mappings + + stub: + """ + touch ${meta.id}.samplesheet.csv + touch ${meta.id}.mappings.csv + """ } From f14ed38ed698d87d0c7b12815ddb878845444e47 Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Tue, 5 May 2026 13:35:34 +0200 Subject: [PATCH 02/11] Handle empty SRA_RUNINFO_TO_FTP output in splitCsv --- workflows/fetchngs.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/workflows/fetchngs.nf b/workflows/fetchngs.nf index e7f1f117..8577510d 100644 --- a/workflows/fetchngs.nf +++ b/workflows/fetchngs.nf @@ -60,6 +60,7 @@ workflow FETCHNGS { SRA_RUNINFO_TO_FTP .out .tsv + .filter { it.size() > 0 } .splitCsv(header:true, sep:'\t') .map { meta -> From 032f6c679ca3bfcd9973c2b63210a8254cb01ebd Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Tue, 5 May 2026 14:14:47 +0200 Subject: [PATCH 03/11] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 525ebc6a..73d1e390 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -190,6 +190,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0 - [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower - [PR #157](https://github.com/nf-core/fetchngs/pull/157) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry +- [PR #368](https://github.com/nf-core/fetchngs/pull/XXX) - Add stub blocks to all local modules ### Software dependencies From 40def90c2c6f917293e5f065c380d15954d9a625 Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Wed, 6 May 2026 14:41:18 +0200 Subject: [PATCH 04/11] Add stub tests to all local modules --- modules/local/aspera_cli/tests/main.nf.test | 27 +++++++++++++++++++ .../tests/main.nf.test | 20 ++++++++++++++ .../local/sra_fastq_ftp/tests/main.nf.test | 26 ++++++++++++++++++ .../sra_ids_to_runinfo/tests/main.nf.test | 21 +++++++++++++++ .../sra_runinfo_to_ftp/tests/main.nf.test | 20 ++++++++++++++ .../sra_to_samplesheet/tests/main.nf.test | 22 +++++++++++++++ 6 files changed, 136 insertions(+) diff --git a/modules/local/aspera_cli/tests/main.nf.test b/modules/local/aspera_cli/tests/main.nf.test index 63347000..2c62a832 100644 --- a/modules/local/aspera_cli/tests/main.nf.test +++ b/modules/local/aspera_cli/tests/main.nf.test @@ -28,4 +28,31 @@ nextflow_process { ) } } + + test("Should run without failures - stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map + [ + 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz', + 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz' + ] + ] + input[1] = 'era-fasp' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test index dbb4d74f..b77a8101 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -21,4 +21,24 @@ nextflow_process { ) } } + + test("Should run without failures - stub") { + + options '-stub' + + when { + process { + """ + input[0] = file(params.pipelines_testdata_base_path + 'csv/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test index bf005290..a669a5c3 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -27,4 +27,30 @@ nextflow_process { ) } } + + test("Should run without failures - stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map + [ + 'ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz', + 'ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz' + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } 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 48797a1a..3602c8c5 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -22,4 +22,25 @@ nextflow_process { ) } } + + test("Should run without failures - stub") { + + options '-stub' + + when { + process { + """ + input[0] = 'SRR13191702' + input[1] = '' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } 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 39db814a..c4e74dd9 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -21,4 +21,24 @@ nextflow_process { ) } } + + test("Should run without failures - stub") { + + options '-stub' + + when { + process { + """ + input[0] = file(params.pipelines_testdata_base_path + 'tsv/SRR13191702.runinfo.tsv', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test index ed765158..e4e1a0e0 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -24,4 +24,26 @@ nextflow_process { ) } } + + test("Should run without failures - stub") { + options '-stub' + + when { + 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] + input[1] = 'rnaseq' + input[2] = 'auto' + input[3] = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } From 469eb92ff458e1df8c7dab8dd6d05533a8bca4b3 Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Wed, 6 May 2026 15:02:00 +0200 Subject: [PATCH 05/11] Add snapshots for local modules --- .../local/aspera_cli/tests/main.nf.test.snap | 95 +++++++------------ .../tests/main.nf.test.snap | 37 +++++++- .../sra_fastq_ftp/tests/main.nf.test.snap | 53 ++++++++--- .../tests/main.nf.test.snap | 37 +++++++- .../tests/main.nf.test.snap | 37 +++++++- .../tests/main.nf.test.snap | 27 +++++- 6 files changed, 204 insertions(+), 82 deletions(-) diff --git a/modules/local/aspera_cli/tests/main.nf.test.snap b/modules/local/aspera_cli/tests/main.nf.test.snap index 7d51292a..48f08d70 100644 --- a/modules/local/aspera_cli/tests/main.nf.test.snap +++ b/modules/local/aspera_cli/tests/main.nf.test.snap @@ -1,80 +1,57 @@ { + "Should run without failures - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + + ], + "fastq": [ + + ], + "md5": [ + + ], + "versions_aspera_cli": [ + + ] + } + ], + "timestamp": "2026-05-06T14:42:22.315537", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, "Should run without failures": { "content": [ { "0": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", - "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" - ] - ] + ], "1": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] + ], "2": [ - [ - "ASPERA_CLI", - "aspera_cli", - "4.14.0" - ] + ], "fastq": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", - "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" - ] - ] + ], "md5": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] + ], "versions_aspera_cli": [ - [ - "ASPERA_CLI", - "aspera_cli", - "4.14.0" - ] + ] } ], - "timestamp": "2026-04-22T14:35:27.716225408", + "timestamp": "2026-05-06T14:42:10.595261", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" 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 776cc5b4..1c9b6d02 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap @@ -1,4 +1,35 @@ { + "Should run without failures - stub": { + "content": [ + { + "0": [ + "multiqc_config.yml:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + [ + "MULTIQC_MAPPINGS_CONFIG", + "python", + "3.10.18" + ] + ], + "versions_python": [ + [ + "MULTIQC_MAPPINGS_CONFIG", + "python", + "3.10.18" + ] + ], + "yml": [ + "multiqc_config.yml:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + } + ], + "timestamp": "2026-05-06T14:42:53.490262", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, "Should run without failures": { "content": [ { @@ -9,14 +40,14 @@ [ "MULTIQC_MAPPINGS_CONFIG", "python", - "3.9.5" + "3.10.18" ] ], "versions_python": [ [ "MULTIQC_MAPPINGS_CONFIG", "python", - "3.9.5" + "3.10.18" ] ], "yml": [ @@ -24,7 +55,7 @@ ] } ], - "timestamp": "2026-04-13T15:41:59.602846", + "timestamp": "2026-05-06T14:42:39.651001", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" 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 c1c750f7..fac070a1 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "Should run without failures": { + "Should run without failures - stub": { "content": [ { "0": [ @@ -11,8 +11,8 @@ "md5_2": "56271be38a80db78ef3bdfc5d9909b98" }, [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", - "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" + "SRX9626017_SRR13191702_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "SRX9626017_SRR13191702_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -25,8 +25,8 @@ "md5_2": "56271be38a80db78ef3bdfc5d9909b98" }, [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -34,7 +34,7 @@ [ "SRA_FASTQ_FTP", "wget", - "1.21.4" + "" ] ], "fastq": [ @@ -46,8 +46,8 @@ "md5_2": "56271be38a80db78ef3bdfc5d9909b98" }, [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", - "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" + "SRX9626017_SRR13191702_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "SRX9626017_SRR13191702_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -60,8 +60,8 @@ "md5_2": "56271be38a80db78ef3bdfc5d9909b98" }, [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -69,12 +69,41 @@ [ "SRA_FASTQ_FTP", "wget", - "1.21.4" + "" ] ] } ], - "timestamp": "2026-04-13T15:42:09.490402", + "timestamp": "2026-05-06T14:43:10.490481", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "Should run without failures": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + + ], + "fastq": [ + + ], + "md5": [ + + ], + "versions_wget": [ + + ] + } + ], + "timestamp": "2026-05-06T14:43:02.233981", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" 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 c4a64afc..1b7d92a2 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 @@ -1,4 +1,35 @@ { + "Should run without failures - stub": { + "content": [ + { + "0": [ + "SRR13191702.runinfo.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + [ + "SRA_IDS_TO_RUNINFO", + "python", + "3.10.18" + ] + ], + "tsv": [ + "SRR13191702.runinfo.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions_python": [ + [ + "SRA_IDS_TO_RUNINFO", + "python", + "3.10.18" + ] + ] + } + ], + "timestamp": "2026-05-06T14:43:29.759674", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, "Should run without failures": { "content": [ { @@ -9,7 +40,7 @@ [ "SRA_IDS_TO_RUNINFO", "python", - "3.9.5" + "3.10.18" ] ], "tsv": [ @@ -19,12 +50,12 @@ [ "SRA_IDS_TO_RUNINFO", "python", - "3.9.5" + "3.10.18" ] ] } ], - "timestamp": "2026-04-13T15:42:19.072989", + "timestamp": "2026-05-06T14:43:21.109568", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" 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 f9cfee1f..bf1ab125 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 @@ -1,4 +1,35 @@ { + "Should run without failures - stub": { + "content": [ + { + "0": [ + "SRR13191702.runinfo_ftp.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + [ + "SRA_RUNINFO_TO_FTP", + "python", + "3.10.18" + ] + ], + "tsv": [ + "SRR13191702.runinfo_ftp.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions_python": [ + [ + "SRA_RUNINFO_TO_FTP", + "python", + "3.10.18" + ] + ] + } + ], + "timestamp": "2026-05-06T14:44:01.816406", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, "Should run without failures": { "content": [ { @@ -9,7 +40,7 @@ [ "SRA_RUNINFO_TO_FTP", "python", - "3.9.5" + "3.10.18" ] ], "tsv": [ @@ -19,12 +50,12 @@ [ "SRA_RUNINFO_TO_FTP", "python", - "3.9.5" + "3.10.18" ] ] } ], - "timestamp": "2026-04-13T15:42:31.518986", + "timestamp": "2026-05-06T14:43:46.204571", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" 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 568f3ea7..5e56b61e 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap @@ -1,4 +1,27 @@ { + "Should run without failures - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "mappings": [ + + ], + "samplesheet": [ + + ] + } + ], + "timestamp": "2026-05-06T14:44:19.343559", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, "Should run without failures": { "content": [ { @@ -108,10 +131,10 @@ ] } ], + "timestamp": "2024-02-28T11:51:38.244046", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T11:51:38.244046" + } } } \ No newline at end of file From 2f181ce2137b4a6de3031a81ae50f2edba136859 Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Wed, 6 May 2026 15:05:13 +0200 Subject: [PATCH 06/11] Remove stub blocks from aspera_cli and sra_to_samplesheet --- modules/local/aspera_cli/main.nf | 14 ---------- modules/local/aspera_cli/tests/main.nf.test | 26 ------------------- modules/local/sra_to_samplesheet/main.nf | 6 ----- .../sra_to_samplesheet/tests/main.nf.test | 21 --------------- 4 files changed, 67 deletions(-) diff --git a/modules/local/aspera_cli/main.nf b/modules/local/aspera_cli/main.nf index 1fbdf641..a8c8d3ba 100644 --- a/modules/local/aspera_cli/main.nf +++ b/modules/local/aspera_cli/main.nf @@ -56,18 +56,4 @@ process ASPERA_CLI { """ } - stub: - if (meta.single_end) { - """ - echo "" | gzip > ${meta.id}.fastq.gz - touch ${meta.id}.fastq.gz.md5 - """ - } else { - """ - echo "" | gzip > ${meta.id}_1.fastq.gz - echo "" | gzip > ${meta.id}_2.fastq.gz - touch ${meta.id}_1.fastq.gz.md5 - touch ${meta.id}_2.fastq.gz.md5 - """ - } } diff --git a/modules/local/aspera_cli/tests/main.nf.test b/modules/local/aspera_cli/tests/main.nf.test index 2c62a832..a4649270 100644 --- a/modules/local/aspera_cli/tests/main.nf.test +++ b/modules/local/aspera_cli/tests/main.nf.test @@ -29,30 +29,4 @@ nextflow_process { } } - test("Should run without failures - stub") { - - options '-stub' - - when { - process { - """ - input[0] = [ - [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map - [ - 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz', - 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz' - ] - ] - input[1] = 'era-fasp' - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } } diff --git a/modules/local/sra_to_samplesheet/main.nf b/modules/local/sra_to_samplesheet/main.nf index 11b6f0d2..92edf5df 100644 --- a/modules/local/sra_to_samplesheet/main.nf +++ b/modules/local/sra_to_samplesheet/main.nf @@ -72,10 +72,4 @@ process SRA_TO_SAMPLESHEET { // Write mappings to file def mappings_file = task.workDir.resolve("${meta.id}.mappings.csv") mappings_file.text = mappings - - stub: - """ - touch ${meta.id}.samplesheet.csv - touch ${meta.id}.mappings.csv - """ } diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test index e4e1a0e0..4fc5f135 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -25,25 +25,4 @@ nextflow_process { } } - test("Should run without failures - stub") { - options '-stub' - - when { - 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] - input[1] = 'rnaseq' - input[2] = 'auto' - input[3] = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description' - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } } From 87148b460cf3a98a88d5631783e75c8e647e0bd7 Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Wed, 6 May 2026 15:27:37 +0200 Subject: [PATCH 07/11] Remove snapshot assertion from stub tests --- modules/local/multiqc_mappings_config/tests/main.nf.test | 4 +--- modules/local/sra_fastq_ftp/tests/main.nf.test | 4 +--- modules/local/sra_ids_to_runinfo/tests/main.nf.test | 4 +--- modules/local/sra_runinfo_to_ftp/tests/main.nf.test | 4 +--- 4 files changed, 4 insertions(+), 12 deletions(-) diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test index b77a8101..e681ad88 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -23,7 +23,6 @@ nextflow_process { } test("Should run without failures - stub") { - options '-stub' when { @@ -36,8 +35,7 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert process.success } ) } } diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test index a669a5c3..88317d46 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -29,7 +29,6 @@ nextflow_process { } test("Should run without failures - stub") { - options '-stub' when { @@ -48,8 +47,7 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert process.success } ) } } 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 3602c8c5..8ea4a642 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -24,7 +24,6 @@ nextflow_process { } test("Should run without failures - stub") { - options '-stub' when { @@ -38,8 +37,7 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert process.success } ) } } 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 c4e74dd9..4a81b136 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -23,7 +23,6 @@ nextflow_process { } test("Should run without failures - stub") { - options '-stub' when { @@ -36,8 +35,7 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert process.success } ) } } From 4f5a8cbf79023c4d25ab88c11a317f5063b1a0c0 Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Wed, 6 May 2026 16:10:47 +0200 Subject: [PATCH 08/11] Update snapshots --- .../tests/main.nf.test.snap | 37 ++----------- .../sra_fastq_ftp/tests/main.nf.test.snap | 53 +++++-------------- .../tests/main.nf.test.snap | 37 ++----------- .../tests/main.nf.test.snap | 37 ++----------- .../tests/main.nf.test.snap | 23 -------- 5 files changed, 21 insertions(+), 166 deletions(-) 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 1c9b6d02..57e5a12f 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap @@ -1,35 +1,4 @@ { - "Should run without failures - stub": { - "content": [ - { - "0": [ - "multiqc_config.yml:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "1": [ - [ - "MULTIQC_MAPPINGS_CONFIG", - "python", - "3.10.18" - ] - ], - "versions_python": [ - [ - "MULTIQC_MAPPINGS_CONFIG", - "python", - "3.10.18" - ] - ], - "yml": [ - "multiqc_config.yml:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - } - ], - "timestamp": "2026-05-06T14:42:53.490262", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - }, "Should run without failures": { "content": [ { @@ -40,14 +9,14 @@ [ "MULTIQC_MAPPINGS_CONFIG", "python", - "3.10.18" + "3.9.5" ] ], "versions_python": [ [ "MULTIQC_MAPPINGS_CONFIG", "python", - "3.10.18" + "3.9.5" ] ], "yml": [ @@ -55,7 +24,7 @@ ] } ], - "timestamp": "2026-05-06T14:42:39.651001", + "timestamp": "2026-05-06T16:00:30.170721088", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" 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 fac070a1..e8f7dea5 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "Should run without failures - stub": { + "Should run without failures": { "content": [ { "0": [ @@ -11,8 +11,8 @@ "md5_2": "56271be38a80db78ef3bdfc5d9909b98" }, [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "SRX9626017_SRR13191702_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", + "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" ] ] ], @@ -25,8 +25,8 @@ "md5_2": "56271be38a80db78ef3bdfc5d9909b98" }, [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e" + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ] ], @@ -34,7 +34,7 @@ [ "SRA_FASTQ_FTP", "wget", - "" + "1.21.4" ] ], "fastq": [ @@ -46,8 +46,8 @@ "md5_2": "56271be38a80db78ef3bdfc5d9909b98" }, [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "SRX9626017_SRR13191702_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", + "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" ] ] ], @@ -60,8 +60,8 @@ "md5_2": "56271be38a80db78ef3bdfc5d9909b98" }, [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e" + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ] ], @@ -69,41 +69,12 @@ [ "SRA_FASTQ_FTP", "wget", - "" + "1.21.4" ] ] } ], - "timestamp": "2026-05-06T14:43:10.490481", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - }, - "Should run without failures": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "2": [ - - ], - "fastq": [ - - ], - "md5": [ - - ], - "versions_wget": [ - - ] - } - ], - "timestamp": "2026-05-06T14:43:02.233981", + "timestamp": "2026-05-06T16:01:04.565094912", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" 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 1b7d92a2..38a5dc6d 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 @@ -1,35 +1,4 @@ { - "Should run without failures - stub": { - "content": [ - { - "0": [ - "SRR13191702.runinfo.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "1": [ - [ - "SRA_IDS_TO_RUNINFO", - "python", - "3.10.18" - ] - ], - "tsv": [ - "SRR13191702.runinfo.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "versions_python": [ - [ - "SRA_IDS_TO_RUNINFO", - "python", - "3.10.18" - ] - ] - } - ], - "timestamp": "2026-05-06T14:43:29.759674", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - }, "Should run without failures": { "content": [ { @@ -40,7 +9,7 @@ [ "SRA_IDS_TO_RUNINFO", "python", - "3.10.18" + "3.9.5" ] ], "tsv": [ @@ -50,12 +19,12 @@ [ "SRA_IDS_TO_RUNINFO", "python", - "3.10.18" + "3.9.5" ] ] } ], - "timestamp": "2026-05-06T14:43:21.109568", + "timestamp": "2026-05-06T16:01:36.028872084", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" 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 bf1ab125..d019854e 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 @@ -1,35 +1,4 @@ { - "Should run without failures - stub": { - "content": [ - { - "0": [ - "SRR13191702.runinfo_ftp.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "1": [ - [ - "SRA_RUNINFO_TO_FTP", - "python", - "3.10.18" - ] - ], - "tsv": [ - "SRR13191702.runinfo_ftp.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "versions_python": [ - [ - "SRA_RUNINFO_TO_FTP", - "python", - "3.10.18" - ] - ] - } - ], - "timestamp": "2026-05-06T14:44:01.816406", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - }, "Should run without failures": { "content": [ { @@ -40,7 +9,7 @@ [ "SRA_RUNINFO_TO_FTP", "python", - "3.10.18" + "3.9.5" ] ], "tsv": [ @@ -50,12 +19,12 @@ [ "SRA_RUNINFO_TO_FTP", "python", - "3.10.18" + "3.9.5" ] ] } ], - "timestamp": "2026-05-06T14:43:46.204571", + "timestamp": "2026-05-06T16:02:10.236064039", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" 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 5e56b61e..33e8847d 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap @@ -1,27 +1,4 @@ { - "Should run without failures - stub": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "mappings": [ - - ], - "samplesheet": [ - - ] - } - ], - "timestamp": "2026-05-06T14:44:19.343559", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - }, "Should run without failures": { "content": [ { From 877e69185aade9f1b8323915452d62df518e8bc0 Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Wed, 6 May 2026 16:46:36 +0200 Subject: [PATCH 09/11] Updated changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 73d1e390..c86f1372 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #325](https://github.com/nf-core/fetchngs/pull/325) - Add wget wait time for retries - [PR #333](https://github.com/nf-core/fetchngs/pull/333) - Add logo - [PR #365](https://github.com/nf-core/fetchngs/pull/365) - Template update for nf-core/tools v3.5.2, including topic channels for version reporting +- [PR #368](https://github.com/nf-core/fetchngs/pull/XXX) - Add stub blocks to all local modules ### Software dependencies @@ -190,7 +191,6 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0 - [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower - [PR #157](https://github.com/nf-core/fetchngs/pull/157) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry -- [PR #368](https://github.com/nf-core/fetchngs/pull/XXX) - Add stub blocks to all local modules ### Software dependencies From d8d7b894f59c1d2e544e0c5e7af03dd9b833e0b1 Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Thu, 7 May 2026 11:25:08 +0200 Subject: [PATCH 10/11] Revert aspera_cli changes --- modules/local/aspera_cli/tests/main.nf.test | 3 +- .../local/aspera_cli/tests/main.nf.test.snap | 95 ++++++++++++------- 2 files changed, 60 insertions(+), 38 deletions(-) diff --git a/modules/local/aspera_cli/tests/main.nf.test b/modules/local/aspera_cli/tests/main.nf.test index a4649270..fe3cb3f6 100644 --- a/modules/local/aspera_cli/tests/main.nf.test +++ b/modules/local/aspera_cli/tests/main.nf.test @@ -28,5 +28,4 @@ nextflow_process { ) } } - -} +} \ No newline at end of file diff --git a/modules/local/aspera_cli/tests/main.nf.test.snap b/modules/local/aspera_cli/tests/main.nf.test.snap index 48f08d70..7d51292a 100644 --- a/modules/local/aspera_cli/tests/main.nf.test.snap +++ b/modules/local/aspera_cli/tests/main.nf.test.snap @@ -1,57 +1,80 @@ { - "Should run without failures - stub": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "2": [ - - ], - "fastq": [ - - ], - "md5": [ - - ], - "versions_aspera_cli": [ - - ] - } - ], - "timestamp": "2026-05-06T14:42:22.315537", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - }, "Should run without failures": { "content": [ { "0": [ - + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", + "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" + ] + ] ], "1": [ - + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] ], "2": [ - + [ + "ASPERA_CLI", + "aspera_cli", + "4.14.0" + ] ], "fastq": [ - + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", + "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" + ] + ] ], "md5": [ - + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] ], "versions_aspera_cli": [ - + [ + "ASPERA_CLI", + "aspera_cli", + "4.14.0" + ] ] } ], - "timestamp": "2026-05-06T14:42:10.595261", + "timestamp": "2026-04-22T14:35:27.716225408", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From dadca1f340a6fd783be4eb0eb52ef780a4d680ee Mon Sep 17 00:00:00 2001 From: Tabea Attig Date: Thu, 7 May 2026 14:31:46 +0200 Subject: [PATCH 11/11] update aspera_cli stubs --- modules/local/aspera_cli/main.nf | 15 +++++++++++++ modules/local/aspera_cli/tests/main.nf.test | 25 +++++++++++++++++++++ modules/local/sra_fastq_ftp/main.nf | 6 ++--- 3 files changed, 43 insertions(+), 3 deletions(-) diff --git a/modules/local/aspera_cli/main.nf b/modules/local/aspera_cli/main.nf index a8c8d3ba..9460e7db 100644 --- a/modules/local/aspera_cli/main.nf +++ b/modules/local/aspera_cli/main.nf @@ -56,4 +56,19 @@ process ASPERA_CLI { """ } + stub: + if (meta.single_end) { + """ + echo | gzip > ${meta.id}.fastq.gz + touch ${meta.id}.fastq.gz.md5 + """ + } else { + """ + echo | gzip > ${meta.id}_1.fastq.gz + echo | gzip > ${meta.id}_2.fastq.gz + touch ${meta.id}_1.fastq.gz.md5 + touch ${meta.id}_2.fastq.gz.md5 + """ + } + } diff --git a/modules/local/aspera_cli/tests/main.nf.test b/modules/local/aspera_cli/tests/main.nf.test index fe3cb3f6..19822f7a 100644 --- a/modules/local/aspera_cli/tests/main.nf.test +++ b/modules/local/aspera_cli/tests/main.nf.test @@ -28,4 +28,29 @@ nextflow_process { ) } } + + test("Should run without failures - stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map + [ + 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz', + 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz' + ] + ] + input[1] = 'era-fasp' + """ + } + } + + then { + assertAll( + { assert process.success } + ) + } + } } \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/main.nf b/modules/local/sra_fastq_ftp/main.nf index 79df44c7..0b077ab4 100644 --- a/modules/local/sra_fastq_ftp/main.nf +++ b/modules/local/sra_fastq_ftp/main.nf @@ -52,13 +52,13 @@ process SRA_FASTQ_FTP { stub: if (meta.single_end) { """ - echo "" | gzip > ${meta.id}.fastq.gz + echo | gzip > ${meta.id}.fastq.gz touch ${meta.id}.fastq.gz.md5 """ } else { """ - echo "" | gzip > ${meta.id}_1.fastq.gz - echo "" | gzip > ${meta.id}_2.fastq.gz + echo | gzip > ${meta.id}_1.fastq.gz + echo | gzip > ${meta.id}_2.fastq.gz touch ${meta.id}_1.fastq.gz.md5 touch ${meta.id}_2.fastq.gz.md5 """