From f85e0321d27fa8e759a19ed39d9347883bd2feab Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 11:04:40 +0100 Subject: [PATCH 1/7] Use relative paths for main script location for nf-test --- modules/local/multiqc_mappings_config/tests/main.nf.test | 2 +- modules/local/sra_fastq_ftp/tests/main.nf.test | 2 +- modules/local/sra_ids_to_runinfo/tests/main.nf.test | 2 +- modules/local/sra_merge_samplesheet/tests/main.nf.test | 2 +- modules/local/sra_runinfo_to_ftp/tests/main.nf.test | 2 +- modules/local/sra_to_samplesheet/tests/main.nf.test | 2 +- workflows/sra/tests/main.nf.test | 2 +- workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 2 +- workflows/sra/tests/sra_force_sratools_download.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 2 +- workflows/sra/tests/sra_skip_fastq_download.nf.test | 2 +- 14 files changed, 14 insertions(+), 14 deletions(-) diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test index 3bf79537..75356197 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: MULTIQC_MAPPINGS_CONFIG" - script "modules/local/multiqc_mappings_config/main.nf" + script "../main.nf" process "MULTIQC_MAPPINGS_CONFIG" tag "modules" tag "modules_local" diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test index 7892d156..ab846e5d 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: SRA_FASTQ_FTP" - script "modules/local/sra_fastq_ftp/main.nf" + script "../main.nf" process "SRA_FASTQ_FTP" tag "modules" tag "modules_local" 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 f8a44086..087f9069 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: SRA_IDS_TO_RUNINFO" - script "modules/local/sra_ids_to_runinfo/main.nf" + script "../main.nf" process "SRA_IDS_TO_RUNINFO" tag "modules" tag "modules_local" diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test index e37039bd..b7c98622 100644 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: SRA_MERGE_SAMPLESHEET" - script "modules/local/sra_merge_samplesheet/main.nf" + script "../main.nf" process "SRA_MERGE_SAMPLESHEET" tag "modules" tag "modules_local" 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 1558ff39..3b1405f9 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: SRA_RUNINFO_TO_FTP" - script "modules/local/sra_runinfo_to_ftp/main.nf" + script "../main.nf" process "SRA_RUNINFO_TO_FTP" tag "modules" tag "modules_local" diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test index b2ec5b11..6094717b 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: SRA_TO_SAMPLESHEET" - script "modules/local/sra_to_samplesheet/main.nf" + script "../main.nf" process "SRA_TO_SAMPLESHEET" tag "modules" tag "modules_local" diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index dcf67105..6b459773 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" 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 04a60471..0d0b85df 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index c669af8d..5cd54142 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" 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 e88e5f63..ef069674 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" 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 63c871ca..4eb57027 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" 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 15a31848..019c9af8 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" 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 4c11d571..dce26b16 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 8cb68641..142e8aff 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" From 3776119a8717fc723bd60188124f9a92943713fa Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 11:05:06 +0100 Subject: [PATCH 2/7] Remove nf-test branch from ci.yml --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 70f7f815..ef127625 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,7 +11,6 @@ on: - master - dev - refactor - - nf-test env: NXF_ANSI_LOG: false From c44000154a7232911c081fa1511639c1ce635dc0 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 11:14:23 +0100 Subject: [PATCH 3/7] Update CHANGELOG and author contributions --- CHANGELOG.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c500efcc..9264eb59 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unpublished Version / DEV] +### Credits + +Special thanks to the following for their contributions to the release: + +- [Adam Talbot](https://github.com/adamrtalbot) +- [Edmund Miller](https://github.com/Emiller88) +- [Esha Joshi](https://github.com/ejseqera) +- [Harshil Patel](https://github.com/drpatelh) +- [James Fellows Yates](https://github.com/jfy133) +- [Maxime Garcia](https://github.com/maxulysse) +- [Rob Syme](https://github.com/robsyme) +- [Sateesh Peri](https://github.com/sateeshperi) + +Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. + +### Enhancements & fixes + +- [PR #XXX](https://github.com/nf-core/fetchngs/pull/XXX) - Use nf-test for all pipeline testing + ### Enhancements & fixes ## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08 @@ -14,8 +33,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 Special thanks to the following for their contributions to the release: - [Adam Talbot](https://github.com/adamrtalbot) +- [Davide Carlson](https://github.com/davidecarlson) - [Harshil Patel](https://github.com/drpatelh) - [Maxime Garcia](https://github.com/maxulysse) +- [MCMandR](https://github.com/MCMandR) - [Rob Syme](https://github.com/robsyme) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. From 46f258fd879870aae381e9db9e6a14e443ad3ef7 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 11:17:42 +0100 Subject: [PATCH 4/7] Add nf-test citation --- CITATIONS.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CITATIONS.md b/CITATIONS.md index 570e7e5b..482d5600 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -37,7 +37,7 @@ - [Synapse](https://pubmed.ncbi.nlm.nih.gov/24071850/) > Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761. PMID: 24071850; PMCID: PMC3950337. -## Software packaging/containerisation tools +## Software packaging/containerisation/testing tools - [Anaconda](https://anaconda.com) @@ -55,6 +55,8 @@ > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. +- [nf-test](https://code.askimed.com/nf-test) + - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. From f65a861e36aa2238295219572480f64bc1249554 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 11:38:23 +0100 Subject: [PATCH 5/7] Remove workflows/nextflow.config --- nextflow.config | 17 ++++++++++------- workflows/nextflow.config | 12 ------------ 2 files changed, 10 insertions(+), 19 deletions(-) delete mode 100644 workflows/nextflow.config diff --git a/nextflow.config b/nextflow.config index 5ad350c9..3589e118 100644 --- a/nextflow.config +++ b/nextflow.config @@ -65,6 +65,16 @@ try { System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") } +// Module specific configs +includeConfig './modules/nf-core/custom/dumpsoftwareversions/nextflow.config' + +// Workflow specific configs +if (params.input_type == 'sra') { + includeConfig './workflows/sra/nextflow.config' +} else if (params.input_type == 'synapse') { + includeConfig './workflows/synapse/nextflow.config' +} + // Load nf-core/fetchngs custom profiles from different institutions. // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! // try { @@ -227,13 +237,6 @@ manifest { doi = 'https://doi.org/10.5281/zenodo.5070524' } -// Module specific configs -// Currently just dumpsoftwareversions -includeConfig 'modules/nf-core/custom/dumpsoftwareversions/nextflow.config' - -// Workflow specific configs -includeConfig 'workflows/nextflow.config' - // Function to ensure that resource requirements don't go beyond // a maximum limit def check_max(obj, type) { diff --git a/workflows/nextflow.config b/workflows/nextflow.config deleted file mode 100644 index d27deb3a..00000000 --- a/workflows/nextflow.config +++ /dev/null @@ -1,12 +0,0 @@ -// Read in specific config relating to workflow. - -switch ( params.input_type ) { - case "sra": - includeConfig './sra/nextflow.config' - break - case "synapse": - includeConfig './synapse/nextflow.config' - break - default: - break -} \ No newline at end of file From 803c473e82be0b7f9d46749aee603f2347c528e8 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 18:43:49 +0100 Subject: [PATCH 6/7] Add nf-test authors to credits for release --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9264eb59..9fbb2013 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,10 +13,12 @@ Special thanks to the following for their contributions to the release: - [Edmund Miller](https://github.com/Emiller88) - [Esha Joshi](https://github.com/ejseqera) - [Harshil Patel](https://github.com/drpatelh) +- [Lukas Forer](https://github.com/lukfor) - [James Fellows Yates](https://github.com/jfy133) - [Maxime Garcia](https://github.com/maxulysse) - [Rob Syme](https://github.com/robsyme) - [Sateesh Peri](https://github.com/sateeshperi) +- [Sebastian Schönherr](https://github.com/seppinho) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. From 9eebe984d5cf799a5c9361a84f1cad71fc7f4354 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 13 Oct 2023 09:43:49 +0100 Subject: [PATCH 7/7] Re-order tags in workflow nf-test files --- workflows/sra/tests/main.nf.test | 4 ++-- workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 4 ++-- workflows/sra/tests/sra_force_sratools_download.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 4 ++-- workflows/sra/tests/sra_skip_fastq_download.nf.test | 4 ++-- 8 files changed, 16 insertions(+), 16 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 6b459773..1595f94d 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_default_parameters" test("Parameters: default") { 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 0d0b85df..ca3d5bd0 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_custom_ena_metadata_fields" test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 5cd54142..f8f6ff5c 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_force_sratools_download" test("Parameters: --force_sratools_download") { 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 ef069674..5a854533 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_nf_core_pipeline_atacseq" test("Parameters: --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 4eb57027..aeb06857 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_nf_core_pipeline_rnaseq" test("Parameters: --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 019c9af8..c460ffbd 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_nf_core_pipeline_taxprofiler" test("Parameters: --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 dce26b16..f90d8958 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_nf_core_pipeline_viralrecon" test("Parameters: --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 142e8aff..8d21a3d9 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_skip_fastq_download" test("Parameters: --skip_fastq_download") {