From 2c0fafdcf83670b72067d6a59506a65f3ffc5f6b Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 11:13:27 +0200 Subject: [PATCH 01/18] Rename assembly_complete_metadata by adding new ending _fixed_study --- ...mbly_complete_metadata_fixed_study.config} | 0 nextflow.config | 2 +- ...bly_complete_metadata_fixed_study.nf.test} | 6 +++--- ...omplete_metadata_fixed_study.nf.test.snap} | 20 +++++-------------- 4 files changed, 9 insertions(+), 19 deletions(-) rename conf/{test_assembly_complete_metadata.config => test_assembly_complete_metadata_fixed_study.config} (100%) rename tests/{assembly_complete_metadata.nf.test => assembly_complete_metadata_fixed_study.nf.test} (89%) rename tests/{assembly_complete_metadata.nf.test.snap => assembly_complete_metadata_fixed_study.nf.test.snap} (77%) diff --git a/conf/test_assembly_complete_metadata.config b/conf/test_assembly_complete_metadata_fixed_study.config similarity index 100% rename from conf/test_assembly_complete_metadata.config rename to conf/test_assembly_complete_metadata_fixed_study.config diff --git a/nextflow.config b/nextflow.config index d3911f83..69d33c9e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -249,7 +249,7 @@ profiles { test_mag_one_contig { includeConfig 'conf/test_mag_one_contig.conf' } test_mag_no_rna_presence { includeConfig 'conf/test_mag_no_rna_presence.conf' } test_mag_no_taxonomy { includeConfig 'conf/test_mag_no_taxonomy.conf' } - test_assembly_complete_metadata { includeConfig 'conf/test_assembly_complete_metadata.config' } + test_assembly_complete_metadata_fixed_study { includeConfig 'conf/test_assembly_complete_metadata_fixed_study.config' } test_assembly_no_study_complete_metadata { includeConfig 'conf/test_assembly_no_study_complete_metadata.config' } test_assembly_no_coverage_single_reads { includeConfig 'conf/test_assembly_no_coverage_single_reads.config' } test_assembly_no_coverage_paired_reads { includeConfig 'conf/test_assembly_no_coverage_paired_reads.config' } diff --git a/tests/assembly_complete_metadata.nf.test b/tests/assembly_complete_metadata_fixed_study.nf.test similarity index 89% rename from tests/assembly_complete_metadata.nf.test rename to tests/assembly_complete_metadata_fixed_study.nf.test index 485c262d..46215ce7 100644 --- a/tests/assembly_complete_metadata.nf.test +++ b/tests/assembly_complete_metadata_fixed_study.nf.test @@ -4,10 +4,10 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "mode_assembly" - tag "test_assembly_complete_metadata" - profile "test_assembly_complete_metadata" + tag "test_assembly_complete_metadata_fixed_study" + profile "test_assembly_complete_metadata_fixed_study" - test("-profile test_assembly_complete_metadata") { + test("-profile test_assembly_complete_metadata_fixed_study") { when { params { diff --git a/tests/assembly_complete_metadata.nf.test.snap b/tests/assembly_complete_metadata_fixed_study.nf.test.snap similarity index 77% rename from tests/assembly_complete_metadata.nf.test.snap rename to tests/assembly_complete_metadata_fixed_study.nf.test.snap index 5085777d..743aff39 100644 --- a/tests/assembly_complete_metadata.nf.test.snap +++ b/tests/assembly_complete_metadata_fixed_study.nf.test.snap @@ -1,5 +1,5 @@ { - "-profile test_assembly_complete_metadata": { + "-profile test_assembly_complete_metadata_fixed_study": { "content": [ 7, { @@ -51,16 +51,6 @@ "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/Assemblies assigned accessions.pdf", - "multiqc/multiqc_plots/pdf/assembly_metadata.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/Assemblies assigned accessions.png", - "multiqc/multiqc_plots/png/assembly_metadata.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/Assemblies assigned accessions.svg", - "multiqc/multiqc_plots/svg/assembly_metadata.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" @@ -71,10 +61,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-10-16T11:08:01.267709", "meta": { - "nf-test": "0.9.2", - "nextflow": "26.04.1" - }, - "timestamp": "2026-10-15T11:45:06.881317" + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } } } \ No newline at end of file From 1f9f5258f542c72b5cfb83d66e0b0d85c49aea79 Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 12:12:28 +0200 Subject: [PATCH 02/18] Stop using fixed study during testing --- ...t_assembly_no_coverage_paired_reads.config | 3 ++- ...t_assembly_no_coverage_single_reads.config | 3 ++- conf/test_assembly_one_contig.config | 3 ++- conf/test_full.config | 3 ++- conf/test_mag_complete_metadata.conf | 3 ++- conf/test_mag_no_coverage_paired_reads.conf | 3 ++- conf/test_mag_no_coverage_single_reads.conf | 3 ++- conf/test_mag_no_quality.conf | 3 ++- conf/test_mag_no_rna_presence.conf | 3 ++- conf/test_mag_no_taxonomy.conf | 3 ++- conf/test_mag_one_contig.conf | 3 ++- ...mbly_no_coverage_paired_reads.nf.test.snap | 23 ++++++---------- ...mbly_no_coverage_single_reads.nf.test.snap | 23 ++++++---------- tests/assembly_one_contig.nf.test.snap | 13 ++++++---- tests/mag_complete_metadata.nf.test.snap | 26 ++++++------------- .../mag_no_coverage_paired_reads.nf.test.snap | 26 ++++++------------- .../mag_no_coverage_single_reads.nf.test.snap | 26 ++++++------------- tests/mag_no_taxonomy.nf.test.snap | 26 ++++++------------- tests/mag_one_contig.nf.test.snap | 13 ++++++---- 19 files changed, 86 insertions(+), 123 deletions(-) diff --git a/conf/test_assembly_no_coverage_paired_reads.config b/conf/test_assembly_no_coverage_paired_reads.config index 65c73e40..d933641b 100644 --- a/conf/test_assembly_no_coverage_paired_reads.config +++ b/conf/test_assembly_no_coverage_paired_reads.config @@ -27,7 +27,8 @@ params { outdir = 'test_output' mode = "metagenomic_assemblies" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" } diff --git a/conf/test_assembly_no_coverage_single_reads.config b/conf/test_assembly_no_coverage_single_reads.config index 814de310..cffc4ce8 100644 --- a/conf/test_assembly_no_coverage_single_reads.config +++ b/conf/test_assembly_no_coverage_single_reads.config @@ -27,7 +27,8 @@ params { outdir = 'test_output' mode = "metagenomic_assemblies" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" } diff --git a/conf/test_assembly_one_contig.config b/conf/test_assembly_one_contig.config index b27784ef..e2bc2700 100644 --- a/conf/test_assembly_one_contig.config +++ b/conf/test_assembly_one_contig.config @@ -27,7 +27,8 @@ params { outdir = 'test_output' mode = "metagenomic_assemblies" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" } diff --git a/conf/test_full.config b/conf/test_full.config index 98d50424..16f6b49c 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -18,7 +18,8 @@ params { input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_multiple_bins_missing_metadata.csv' mode = "mags" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" test_upload = true diff --git a/conf/test_mag_complete_metadata.conf b/conf/test_mag_complete_metadata.conf index 428878a3..8dfe715e 100644 --- a/conf/test_mag_complete_metadata.conf +++ b/conf/test_mag_complete_metadata.conf @@ -26,7 +26,8 @@ params { input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_complete_metadata.csv' mode = "mags" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" test_upload = true diff --git a/conf/test_mag_no_coverage_paired_reads.conf b/conf/test_mag_no_coverage_paired_reads.conf index 954a9a21..50420200 100644 --- a/conf/test_mag_no_coverage_paired_reads.conf +++ b/conf/test_mag_no_coverage_paired_reads.conf @@ -26,7 +26,8 @@ params { input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_coverage_paired_reads.csv' mode = "mags" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" test_upload = true diff --git a/conf/test_mag_no_coverage_single_reads.conf b/conf/test_mag_no_coverage_single_reads.conf index 48924241..07feea47 100644 --- a/conf/test_mag_no_coverage_single_reads.conf +++ b/conf/test_mag_no_coverage_single_reads.conf @@ -26,7 +26,8 @@ params { input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_coverage_single_reads.csv' mode = "mags" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" test_upload = true diff --git a/conf/test_mag_no_quality.conf b/conf/test_mag_no_quality.conf index 656bffea..b396a521 100644 --- a/conf/test_mag_no_quality.conf +++ b/conf/test_mag_no_quality.conf @@ -26,7 +26,8 @@ params { input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_quality.csv' mode = "mags" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" test_upload = true diff --git a/conf/test_mag_no_rna_presence.conf b/conf/test_mag_no_rna_presence.conf index 1577455b..18d489d1 100644 --- a/conf/test_mag_no_rna_presence.conf +++ b/conf/test_mag_no_rna_presence.conf @@ -26,7 +26,8 @@ params { input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_rna_presence.csv' mode = "mags" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" test_upload = true diff --git a/conf/test_mag_no_taxonomy.conf b/conf/test_mag_no_taxonomy.conf index bb9f6870..fbb373cb 100644 --- a/conf/test_mag_no_taxonomy.conf +++ b/conf/test_mag_no_taxonomy.conf @@ -26,7 +26,8 @@ params { input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_taxonomy.csv' mode = "mags" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" test_upload = true diff --git a/conf/test_mag_one_contig.conf b/conf/test_mag_one_contig.conf index d9f57020..336eb776 100644 --- a/conf/test_mag_one_contig.conf +++ b/conf/test_mag_one_contig.conf @@ -26,7 +26,8 @@ params { input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_one_contig.csv' mode = "mags" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" test_upload = true diff --git a/tests/assembly_no_coverage_paired_reads.nf.test.snap b/tests/assembly_no_coverage_paired_reads.nf.test.snap index 79f3702b..120a027b 100644 --- a/tests/assembly_no_coverage_paired_reads.nf.test.snap +++ b/tests/assembly_no_coverage_paired_reads.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_assembly_no_coverage_paired_reads": { "content": [ - 8, + 9, { "CONCAT_ACCESSIONS": { "coreutils": 9.4, @@ -25,6 +25,9 @@ "GENERATE_ASSEMBLY_MANIFEST": { "assembly_uploader": "1.3.6" }, + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "SUBMIT": { "ena-webin-cli": "9.0.3", "mgnify-pipelines-toolkit": "1.5.1", @@ -56,16 +59,6 @@ "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/Assemblies assigned accessions.pdf", - "multiqc/multiqc_plots/pdf/assembly_metadata.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/Assemblies assigned accessions.png", - "multiqc/multiqc_plots/png/assembly_metadata.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/Assemblies assigned accessions.svg", - "multiqc/multiqc_plots/svg/assembly_metadata.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" @@ -77,10 +70,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-10-15T15:39:15.438257", "meta": { - "nf-test": "0.9.2", - "nextflow": "26.04.1" - }, - "timestamp": "2026-10-15T11:45:06.881317" + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } } } \ No newline at end of file diff --git a/tests/assembly_no_coverage_single_reads.nf.test.snap b/tests/assembly_no_coverage_single_reads.nf.test.snap index 4d754215..0bad315a 100644 --- a/tests/assembly_no_coverage_single_reads.nf.test.snap +++ b/tests/assembly_no_coverage_single_reads.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_assembly_no_coverage_single_reads": { "content": [ - 8, + 9, { "CONCAT_ACCESSIONS": { "coreutils": 9.4, @@ -25,6 +25,9 @@ "GENERATE_ASSEMBLY_MANIFEST": { "assembly_uploader": "1.3.6" }, + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "SUBMIT": { "ena-webin-cli": "9.0.3", "mgnify-pipelines-toolkit": "1.5.1", @@ -56,16 +59,6 @@ "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/Assemblies assigned accessions.pdf", - "multiqc/multiqc_plots/pdf/assembly_metadata.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/Assemblies assigned accessions.png", - "multiqc/multiqc_plots/png/assembly_metadata.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/Assemblies assigned accessions.svg", - "multiqc/multiqc_plots/svg/assembly_metadata.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" @@ -77,10 +70,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-10-15T16:34:10.672881", "meta": { - "nf-test": "0.9.2", - "nextflow": "26.04.1" - }, - "timestamp": "2026-10-15T11:45:06.881317" + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } } } \ No newline at end of file diff --git a/tests/assembly_one_contig.nf.test.snap b/tests/assembly_one_contig.nf.test.snap index 5661f98d..2d7c491e 100644 --- a/tests/assembly_one_contig.nf.test.snap +++ b/tests/assembly_one_contig.nf.test.snap @@ -1,8 +1,11 @@ { "-profile test_assembly_one_contig": { "content": [ - 1, + 2, { + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "Workflow": { "nf-core/seqsubmit": "v1.0.0" } @@ -28,10 +31,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-10-15T16:17:10.488596", "meta": { - "nf-test": "0.9.2", - "nextflow": "26.04.1" - }, - "timestamp": "2026-05-14T10:39:20.087785" + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } } } \ No newline at end of file diff --git a/tests/mag_complete_metadata.nf.test.snap b/tests/mag_complete_metadata.nf.test.snap index 54957593..8a2e8f11 100644 --- a/tests/mag_complete_metadata.nf.test.snap +++ b/tests/mag_complete_metadata.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_mag_complete_metadata": { "content": [ - 7, + 8, { "CONCAT_ACCESSIONS": { "coreutils": 9.4, @@ -22,6 +22,9 @@ "FALINT": { "falint": "1.2.0" }, + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "SUBMIT": { "ena-webin-cli": "9.0.3", "mgnify-pipelines-toolkit": "1.5.1", @@ -59,19 +62,6 @@ "multiqc/multiqc_data/multiqc_sample_registration.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf", - "multiqc/multiqc_plots/pdf/genome_metadata.pdf", - "multiqc/multiqc_plots/pdf/sample_registration.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/Genomes assigned accessions.png", - "multiqc/multiqc_plots/png/genome_metadata.png", - "multiqc/multiqc_plots/png/sample_registration.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/Genomes assigned accessions.svg", - "multiqc/multiqc_plots/svg/genome_metadata.svg", - "multiqc/multiqc_plots/svg/sample_registration.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" @@ -82,10 +72,10 @@ "multiqc_genome_metadata.txt:md5,4364c96b13eb232b290c9f29b0edcf5a" ] ], + "timestamp": "2026-10-16T11:24:05.697224", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.0" - }, - "timestamp": "2026-06-24T16:02:07.683194" + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } } } \ No newline at end of file diff --git a/tests/mag_no_coverage_paired_reads.nf.test.snap b/tests/mag_no_coverage_paired_reads.nf.test.snap index 0725d600..ea4916bd 100644 --- a/tests/mag_no_coverage_paired_reads.nf.test.snap +++ b/tests/mag_no_coverage_paired_reads.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_mag_no_coverage_paired_reads": { "content": [ - 8, + 9, { "CONCAT_ACCESSIONS": { "coreutils": 9.4, @@ -25,6 +25,9 @@ "FALINT": { "falint": "1.2.0" }, + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "SUBMIT": { "ena-webin-cli": "9.0.3", "mgnify-pipelines-toolkit": "1.5.1", @@ -64,19 +67,6 @@ "multiqc/multiqc_data/multiqc_sample_registration.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf", - "multiqc/multiqc_plots/pdf/genome_metadata.pdf", - "multiqc/multiqc_plots/pdf/sample_registration.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/Genomes assigned accessions.png", - "multiqc/multiqc_plots/png/genome_metadata.png", - "multiqc/multiqc_plots/png/sample_registration.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/Genomes assigned accessions.svg", - "multiqc/multiqc_plots/svg/genome_metadata.svg", - "multiqc/multiqc_plots/svg/sample_registration.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" @@ -88,10 +78,10 @@ "multiqc_genome_metadata.txt:md5,73ca3eaa259e29711518c466246aeed5" ] ], + "timestamp": "2026-10-16T11:28:13.637453", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.0" - }, - "timestamp": "2026-06-24T16:04:05.724269" + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } } } \ No newline at end of file diff --git a/tests/mag_no_coverage_single_reads.nf.test.snap b/tests/mag_no_coverage_single_reads.nf.test.snap index 3a432618..f2008f6a 100644 --- a/tests/mag_no_coverage_single_reads.nf.test.snap +++ b/tests/mag_no_coverage_single_reads.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_mag_no_coverage_single_reads": { "content": [ - 8, + 9, { "CONCAT_ACCESSIONS": { "coreutils": 9.4, @@ -25,6 +25,9 @@ "FALINT": { "falint": "1.2.0" }, + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "SUBMIT": { "ena-webin-cli": "9.0.3", "mgnify-pipelines-toolkit": "1.5.1", @@ -64,19 +67,6 @@ "multiqc/multiqc_data/multiqc_sample_registration.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf", - "multiqc/multiqc_plots/pdf/genome_metadata.pdf", - "multiqc/multiqc_plots/pdf/sample_registration.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/Genomes assigned accessions.png", - "multiqc/multiqc_plots/png/genome_metadata.png", - "multiqc/multiqc_plots/png/sample_registration.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/Genomes assigned accessions.svg", - "multiqc/multiqc_plots/svg/genome_metadata.svg", - "multiqc/multiqc_plots/svg/sample_registration.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" @@ -88,10 +78,10 @@ "multiqc_genome_metadata.txt:md5,f87520e8673df42da7971d6b4723d020" ] ], + "timestamp": "2026-10-16T11:59:29.524504", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.0" - }, - "timestamp": "2026-06-24T16:06:35.115481" + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } } } \ No newline at end of file diff --git a/tests/mag_no_taxonomy.nf.test.snap b/tests/mag_no_taxonomy.nf.test.snap index 0aa4bc4d..fc5cc526 100644 --- a/tests/mag_no_taxonomy.nf.test.snap +++ b/tests/mag_no_taxonomy.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_mag_no_taxonomy": { "content": [ - 11, + 12, { "CATPACK_ADDNAMES_BINS": { "catpack": 6.0 @@ -31,6 +31,9 @@ "FALINT": { "falint": "1.2.0" }, + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "RENAME_FASTA_FOR_CATPACK": { "bash": "5.2.37(1)-release" }, @@ -74,19 +77,6 @@ "multiqc/multiqc_data/multiqc_sample_registration.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf", - "multiqc/multiqc_plots/pdf/genome_metadata.pdf", - "multiqc/multiqc_plots/pdf/sample_registration.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/Genomes assigned accessions.png", - "multiqc/multiqc_plots/png/genome_metadata.png", - "multiqc/multiqc_plots/png/sample_registration.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/Genomes assigned accessions.svg", - "multiqc/multiqc_plots/svg/genome_metadata.svg", - "multiqc/multiqc_plots/svg/sample_registration.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" @@ -99,10 +89,10 @@ "multiqc_genome_metadata.txt:md5,c2bdf8ba36b55b5f48fa07a26e5222f5" ] ], + "timestamp": "2026-10-15T16:23:14.854681", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.0" - }, - "timestamp": "2026-06-24T16:20:51.581304" + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } } } \ No newline at end of file diff --git a/tests/mag_one_contig.nf.test.snap b/tests/mag_one_contig.nf.test.snap index 1181faee..b3cb0c02 100644 --- a/tests/mag_one_contig.nf.test.snap +++ b/tests/mag_one_contig.nf.test.snap @@ -1,8 +1,11 @@ { "-profile test_mag_one_contig": { "content": [ - 1, + 2, { + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "Workflow": { "nf-core/seqsubmit": "v1.0.0" } @@ -28,10 +31,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], + "timestamp": "2026-10-15T16:19:46.817973", "meta": { - "nf-test": "0.9.2", - "nextflow": "26.04.1" - }, - "timestamp": "2026-05-14T10:59:16.375369" + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } } } \ No newline at end of file From 56dcd0342e3bded0efdaf251405ded84f5eb5802 Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 12:14:19 +0200 Subject: [PATCH 03/18] Ignore .venv --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index effbc73d..7540f78c 100644 --- a/.gitignore +++ b/.gitignore @@ -11,3 +11,4 @@ null/ .nf-test* .idea/ test_data +.venv From 6a948eb0270fd97a0508c75e237621df6b2e7b5a Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 15:20:28 +0200 Subject: [PATCH 04/18] Hard-code project accession (reverting previous edit) --- conf/test_mag_complete_metadata.conf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/conf/test_mag_complete_metadata.conf b/conf/test_mag_complete_metadata.conf index 8dfe715e..428878a3 100644 --- a/conf/test_mag_complete_metadata.conf +++ b/conf/test_mag_complete_metadata.conf @@ -26,8 +26,7 @@ params { input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_complete_metadata.csv' mode = "mags" - submission_study = null - study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' + submission_study = "PRJEB98843" centre_name = "TEST_CENTER" test_upload = true From c208e7fa5754da5911bf03bf52563447f8c22038 Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 15:36:51 +0200 Subject: [PATCH 05/18] Rename test mag_complete_metadata to mag_complete_metadata_fixed_study --- ....conf => test_mag_complete_metadata_fixed_study.conf} | 0 nextflow.config | 2 +- ...nf.test => mag_complete_metadata_fixed_study.nf.test} | 6 +++--- ...ap => mag_complete_metadata_fixed_study.nf.test.snap} | 9 +++------ 4 files changed, 7 insertions(+), 10 deletions(-) rename conf/{test_mag_complete_metadata.conf => test_mag_complete_metadata_fixed_study.conf} (100%) rename tests/{mag_complete_metadata.nf.test => mag_complete_metadata_fixed_study.nf.test} (89%) rename tests/{mag_complete_metadata.nf.test.snap => mag_complete_metadata_fixed_study.nf.test.snap} (93%) diff --git a/conf/test_mag_complete_metadata.conf b/conf/test_mag_complete_metadata_fixed_study.conf similarity index 100% rename from conf/test_mag_complete_metadata.conf rename to conf/test_mag_complete_metadata_fixed_study.conf diff --git a/nextflow.config b/nextflow.config index 69d33c9e..582a9fe5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -241,7 +241,7 @@ profiles { } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } - test_mag_complete_metadata { includeConfig 'conf/test_mag_complete_metadata.conf' } + test_mag_complete_metadata_fixed_study { includeConfig 'conf/test_mag_complete_metadata_fixed_study.conf' } test_mag_no_study_complete_metadata { includeConfig 'conf/test_mag_no_study_complete_metadata.config' } test_mag_no_coverage_single_reads { includeConfig 'conf/test_mag_no_coverage_single_reads.conf' } test_mag_no_coverage_paired_reads { includeConfig 'conf/test_mag_no_coverage_paired_reads.conf' } diff --git a/tests/mag_complete_metadata.nf.test b/tests/mag_complete_metadata_fixed_study.nf.test similarity index 89% rename from tests/mag_complete_metadata.nf.test rename to tests/mag_complete_metadata_fixed_study.nf.test index 9b428487..484e1fbe 100644 --- a/tests/mag_complete_metadata.nf.test +++ b/tests/mag_complete_metadata_fixed_study.nf.test @@ -4,10 +4,10 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "mode_mag" - tag "test_mag_complete_metadata" - profile "test_mag_complete_metadata" + tag "test_mag_complete_metadata_fixed_study" + profile "test_mag_complete_metadata_fixed_study" - test("-profile test_mag_complete_metadata") { + test("-profile test_mag_complete_metadata_fixed_study") { when { params { diff --git a/tests/mag_complete_metadata.nf.test.snap b/tests/mag_complete_metadata_fixed_study.nf.test.snap similarity index 93% rename from tests/mag_complete_metadata.nf.test.snap rename to tests/mag_complete_metadata_fixed_study.nf.test.snap index 8a2e8f11..1c5b8926 100644 --- a/tests/mag_complete_metadata.nf.test.snap +++ b/tests/mag_complete_metadata_fixed_study.nf.test.snap @@ -1,7 +1,7 @@ { - "-profile test_mag_complete_metadata": { + "-profile test_mag_complete_metadata_fixed_study": { "content": [ - 8, + 7, { "CONCAT_ACCESSIONS": { "coreutils": 9.4, @@ -22,9 +22,6 @@ "FALINT": { "falint": "1.2.0" }, - "REGISTERSTUDY": { - "mgnify-pipelines-toolkit": "1.5.1" - }, "SUBMIT": { "ena-webin-cli": "9.0.3", "mgnify-pipelines-toolkit": "1.5.1", @@ -72,7 +69,7 @@ "multiqc_genome_metadata.txt:md5,4364c96b13eb232b290c9f29b0edcf5a" ] ], - "timestamp": "2026-10-16T11:24:05.697224", + "timestamp": "2026-10-16T15:32:26.944716", "meta": { "nf-test": "0.9.5", "nextflow": "26.10.0" From bb03d81977803cc4bbc59549610f37ca138f5718 Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 15:46:37 +0200 Subject: [PATCH 06/18] Rename test mag_no_study_complete_metadata to mag_complete_metadata --- ...nfig => test_mag_complete_metadata.config} | 0 nextflow.config | 2 +- ....nf.test => mag_complete_metadata.nf.test} | 6 +- ...nap => mag_complete_metadata.nf.test.snap} | 83 ++++++++++++++++++- 4 files changed, 85 insertions(+), 6 deletions(-) rename conf/{test_mag_no_study_complete_metadata.config => test_mag_complete_metadata.config} (100%) rename tests/{mag_no_study_complete_metadata.nf.test => mag_complete_metadata.nf.test} (90%) rename tests/{mag_no_study_complete_metadata.nf.test.snap => mag_complete_metadata.nf.test.snap} (54%) diff --git a/conf/test_mag_no_study_complete_metadata.config b/conf/test_mag_complete_metadata.config similarity index 100% rename from conf/test_mag_no_study_complete_metadata.config rename to conf/test_mag_complete_metadata.config diff --git a/nextflow.config b/nextflow.config index 582a9fe5..f4f8bfcf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -242,7 +242,7 @@ profiles { test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } test_mag_complete_metadata_fixed_study { includeConfig 'conf/test_mag_complete_metadata_fixed_study.conf' } - test_mag_no_study_complete_metadata { includeConfig 'conf/test_mag_no_study_complete_metadata.config' } + test_mag_complete_metadata { includeConfig 'conf/test_mag_complete_metadata.config' } test_mag_no_coverage_single_reads { includeConfig 'conf/test_mag_no_coverage_single_reads.conf' } test_mag_no_coverage_paired_reads { includeConfig 'conf/test_mag_no_coverage_paired_reads.conf' } test_mag_no_quality { includeConfig 'conf/test_mag_no_quality.conf' } diff --git a/tests/mag_no_study_complete_metadata.nf.test b/tests/mag_complete_metadata.nf.test similarity index 90% rename from tests/mag_no_study_complete_metadata.nf.test rename to tests/mag_complete_metadata.nf.test index d585286f..9b428487 100644 --- a/tests/mag_no_study_complete_metadata.nf.test +++ b/tests/mag_complete_metadata.nf.test @@ -4,10 +4,10 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "mode_mag" - tag "test_mag_no_study_complete_metadata" - profile "test_mag_no_study_complete_metadata" + tag "test_mag_complete_metadata" + profile "test_mag_complete_metadata" - test("-profile test_mag_no_study_complete_metadata") { + test("-profile test_mag_complete_metadata") { when { params { diff --git a/tests/mag_no_study_complete_metadata.nf.test.snap b/tests/mag_complete_metadata.nf.test.snap similarity index 54% rename from tests/mag_no_study_complete_metadata.nf.test.snap rename to tests/mag_complete_metadata.nf.test.snap index b838f6b5..f70e95e7 100644 --- a/tests/mag_no_study_complete_metadata.nf.test.snap +++ b/tests/mag_complete_metadata.nf.test.snap @@ -1,4 +1,83 @@ { + "-profile test_mag_complete_metadata": { + "content": [ + 8, + { + "CONCAT_ACCESSIONS": { + "coreutils": 9.4, + "find": "4.6.0", + "pigz": 2.8 + }, + "CONCAT_METADATA": { + "coreutils": 9.4, + "find": "4.6.0", + "pigz": 2.8 + }, + "CREATE_GENOME_METADATA_TSV": { + "bash": "5.2.37(1)-release" + }, + "CREATE_MANIFESTS": { + "genome_uploader": "3.0.4" + }, + "FALINT": { + "falint": "1.2.0" + }, + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, + "SUBMIT": { + "ena-webin-cli": "9.0.3", + "mgnify-pipelines-toolkit": "1.5.1", + "python": "3.12.13" + }, + "Workflow": { + "nf-core/seqsubmit": "v1.0.0" + } + }, + [ + "mags", + "mags/complete_metadata", + "mags/complete_metadata/upload", + "mags/complete_metadata/upload/webin_cli", + "mags/complete_metadata/upload/webin_cli/complete_metadata_accessions.tsv", + "mags/upload", + "mags/upload/genomes_accessions.tsv", + "mags/upload/genomes_metadata.tsv", + "mags/upload/manifests", + "mags/upload/manifests/results", + "mags/upload/manifests/results/MAG_upload", + "mags/upload/manifests/results/MAG_upload/ENA_backup.json", + "mags/upload/manifests/results/MAG_upload/genome_samples.xml", + "mags/upload/manifests/results/MAG_upload/manifests_test", + "mags/upload/manifests/results/MAG_upload/registered_MAGs_test.tsv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_Genomes assigned accessions.txt", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_genome_metadata.txt", + "multiqc/multiqc_data/multiqc_sample_registration.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" + ], + [ + "genomes_metadata.tsv:md5,ae2b884015d1850fa63365e8a64d9fc8", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_genome_metadata.txt:md5,4364c96b13eb232b290c9f29b0edcf5a" + ] + ], + "timestamp": "2026-10-16T15:45:00.14863", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } + }, "-profile test_mag_no_study_complete_metadata": { "content": [ 8, @@ -85,10 +164,10 @@ "multiqc_genome_metadata.txt:md5,4364c96b13eb232b290c9f29b0edcf5a" ] ], + "timestamp": "2026-06-24T19:28:10.097952", "meta": { "nf-test": "0.9.3", "nextflow": "26.04.0" - }, - "timestamp": "2026-06-24T19:28:10.097952" + } } } \ No newline at end of file From c3942d4277bbd7fe92974b1d811b6ef061a7d678 Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 12:30:27 +0100 Subject: [PATCH 07/18] align brackets in nextflow.config --- nextflow.config | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/nextflow.config b/nextflow.config index f4f8bfcf..e420a539 100644 --- a/nextflow.config +++ b/nextflow.config @@ -239,22 +239,22 @@ profiles { apptainer.runOptions = '--nv' singularity.runOptions = '--nv' } - test { includeConfig 'conf/test.config' } - test_full { includeConfig 'conf/test_full.config' } - test_mag_complete_metadata_fixed_study { includeConfig 'conf/test_mag_complete_metadata_fixed_study.conf' } - test_mag_complete_metadata { includeConfig 'conf/test_mag_complete_metadata.config' } - test_mag_no_coverage_single_reads { includeConfig 'conf/test_mag_no_coverage_single_reads.conf' } - test_mag_no_coverage_paired_reads { includeConfig 'conf/test_mag_no_coverage_paired_reads.conf' } - test_mag_no_quality { includeConfig 'conf/test_mag_no_quality.conf' } - test_mag_one_contig { includeConfig 'conf/test_mag_one_contig.conf' } - test_mag_no_rna_presence { includeConfig 'conf/test_mag_no_rna_presence.conf' } - test_mag_no_taxonomy { includeConfig 'conf/test_mag_no_taxonomy.conf' } + test { includeConfig 'conf/test.config' } + test_full { includeConfig 'conf/test_full.config' } + test_mag_complete_metadata_fixed_study { includeConfig 'conf/test_mag_complete_metadata_fixed_study.conf' } + test_mag_complete_metadata { includeConfig 'conf/test_mag_complete_metadata.config' } + test_mag_no_coverage_single_reads { includeConfig 'conf/test_mag_no_coverage_single_reads.conf' } + test_mag_no_coverage_paired_reads { includeConfig 'conf/test_mag_no_coverage_paired_reads.conf' } + test_mag_no_quality { includeConfig 'conf/test_mag_no_quality.conf' } + test_mag_one_contig { includeConfig 'conf/test_mag_one_contig.conf' } + test_mag_no_rna_presence { includeConfig 'conf/test_mag_no_rna_presence.conf' } + test_mag_no_taxonomy { includeConfig 'conf/test_mag_no_taxonomy.conf' } test_assembly_complete_metadata_fixed_study { includeConfig 'conf/test_assembly_complete_metadata_fixed_study.config' } - test_assembly_no_study_complete_metadata { includeConfig 'conf/test_assembly_no_study_complete_metadata.config' } - test_assembly_no_coverage_single_reads { includeConfig 'conf/test_assembly_no_coverage_single_reads.config' } - test_assembly_no_coverage_paired_reads { includeConfig 'conf/test_assembly_no_coverage_paired_reads.config' } - test_assembly_one_contig { includeConfig 'conf/test_assembly_one_contig.config' } - test_reads_paired { includeConfig 'conf/test_reads_paired.config' } + test_assembly_complete_metadata { includeConfig 'conf/test_assembly_complete_metadata.config' } + test_assembly_no_coverage_single_reads { includeConfig 'conf/test_assembly_no_coverage_single_reads.config' } + test_assembly_no_coverage_paired_reads { includeConfig 'conf/test_assembly_no_coverage_paired_reads.config' } + test_assembly_one_contig { includeConfig 'conf/test_assembly_one_contig.config' } + test_reads_paired { includeConfig 'conf/test_reads_paired.config' } } // Load nf-core custom profiles from different institutions From 06dd5f858a8170b72ecc6f3b4f84a50ce63460ad Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 12:32:53 +0100 Subject: [PATCH 08/18] rename test --- ...tadata.config => test_assembly_complete_metadata.config} | 0 ..._metadata.nf.test => assembly_complete_metadata.nf.test} | 6 +++--- ...nf.test.snap => assembly_complete_metadata.nf.test.snap} | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) rename conf/{test_assembly_no_study_complete_metadata.config => test_assembly_complete_metadata.config} (100%) rename tests/{assembly_no_study_complete_metadata.nf.test => assembly_complete_metadata.nf.test} (89%) rename tests/{assembly_no_study_complete_metadata.nf.test.snap => assembly_complete_metadata.nf.test.snap} (98%) diff --git a/conf/test_assembly_no_study_complete_metadata.config b/conf/test_assembly_complete_metadata.config similarity index 100% rename from conf/test_assembly_no_study_complete_metadata.config rename to conf/test_assembly_complete_metadata.config diff --git a/tests/assembly_no_study_complete_metadata.nf.test b/tests/assembly_complete_metadata.nf.test similarity index 89% rename from tests/assembly_no_study_complete_metadata.nf.test rename to tests/assembly_complete_metadata.nf.test index 09c9f0be..485c262d 100644 --- a/tests/assembly_no_study_complete_metadata.nf.test +++ b/tests/assembly_complete_metadata.nf.test @@ -4,10 +4,10 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "mode_assembly" - tag "test_assembly_no_study_complete_metadata" - profile "test_assembly_no_study_complete_metadata" + tag "test_assembly_complete_metadata" + profile "test_assembly_complete_metadata" - test("-profile test_assembly_no_study_complete_metadata") { + test("-profile test_assembly_complete_metadata") { when { params { diff --git a/tests/assembly_no_study_complete_metadata.nf.test.snap b/tests/assembly_complete_metadata.nf.test.snap similarity index 98% rename from tests/assembly_no_study_complete_metadata.nf.test.snap rename to tests/assembly_complete_metadata.nf.test.snap index 27be885e..1221e619 100644 --- a/tests/assembly_no_study_complete_metadata.nf.test.snap +++ b/tests/assembly_complete_metadata.nf.test.snap @@ -1,5 +1,5 @@ { - "-profile test_assembly_no_study_complete_metadata": { + "-profile test_assembly_complete_metadata": { "content": [ 8, { From b7dda6fc06b5f0ccb2a10eb4a602b8e9a42f0e83 Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 12:33:11 +0100 Subject: [PATCH 09/18] update snapshots --- ...embly_complete_metadata_fixed_study.nf.test.snap | 10 ++++++++++ .../assembly_no_coverage_paired_reads.nf.test.snap | 10 ++++++++++ .../assembly_no_coverage_single_reads.nf.test.snap | 10 ++++++++++ tests/mag_complete_metadata.nf.test.snap | 13 +++++++++++++ .../mag_complete_metadata_fixed_study.nf.test.snap | 13 +++++++++++++ tests/mag_no_coverage_paired_reads.nf.test.snap | 13 +++++++++++++ tests/mag_no_coverage_single_reads.nf.test.snap | 13 +++++++++++++ tests/mag_no_taxonomy.nf.test.snap | 13 +++++++++++++ 8 files changed, 95 insertions(+) diff --git a/tests/assembly_complete_metadata_fixed_study.nf.test.snap b/tests/assembly_complete_metadata_fixed_study.nf.test.snap index 743aff39..ce607e8a 100644 --- a/tests/assembly_complete_metadata_fixed_study.nf.test.snap +++ b/tests/assembly_complete_metadata_fixed_study.nf.test.snap @@ -51,6 +51,16 @@ "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/Assemblies assigned accessions.pdf", + "multiqc/multiqc_plots/pdf/assembly_metadata.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/Assemblies assigned accessions.png", + "multiqc/multiqc_plots/png/assembly_metadata.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/Assemblies assigned accessions.svg", + "multiqc/multiqc_plots/svg/assembly_metadata.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" diff --git a/tests/assembly_no_coverage_paired_reads.nf.test.snap b/tests/assembly_no_coverage_paired_reads.nf.test.snap index 120a027b..b898bf04 100644 --- a/tests/assembly_no_coverage_paired_reads.nf.test.snap +++ b/tests/assembly_no_coverage_paired_reads.nf.test.snap @@ -59,6 +59,16 @@ "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/Assemblies assigned accessions.pdf", + "multiqc/multiqc_plots/pdf/assembly_metadata.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/Assemblies assigned accessions.png", + "multiqc/multiqc_plots/png/assembly_metadata.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/Assemblies assigned accessions.svg", + "multiqc/multiqc_plots/svg/assembly_metadata.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" diff --git a/tests/assembly_no_coverage_single_reads.nf.test.snap b/tests/assembly_no_coverage_single_reads.nf.test.snap index 0bad315a..539dd28f 100644 --- a/tests/assembly_no_coverage_single_reads.nf.test.snap +++ b/tests/assembly_no_coverage_single_reads.nf.test.snap @@ -59,6 +59,16 @@ "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/Assemblies assigned accessions.pdf", + "multiqc/multiqc_plots/pdf/assembly_metadata.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/Assemblies assigned accessions.png", + "multiqc/multiqc_plots/png/assembly_metadata.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/Assemblies assigned accessions.svg", + "multiqc/multiqc_plots/svg/assembly_metadata.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" diff --git a/tests/mag_complete_metadata.nf.test.snap b/tests/mag_complete_metadata.nf.test.snap index f70e95e7..1a8dd07d 100644 --- a/tests/mag_complete_metadata.nf.test.snap +++ b/tests/mag_complete_metadata.nf.test.snap @@ -62,6 +62,19 @@ "multiqc/multiqc_data/multiqc_sample_registration.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf", + "multiqc/multiqc_plots/pdf/genome_metadata.pdf", + "multiqc/multiqc_plots/pdf/sample_registration.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/Genomes assigned accessions.png", + "multiqc/multiqc_plots/png/genome_metadata.png", + "multiqc/multiqc_plots/png/sample_registration.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/Genomes assigned accessions.svg", + "multiqc/multiqc_plots/svg/genome_metadata.svg", + "multiqc/multiqc_plots/svg/sample_registration.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" diff --git a/tests/mag_complete_metadata_fixed_study.nf.test.snap b/tests/mag_complete_metadata_fixed_study.nf.test.snap index 1c5b8926..5786f91e 100644 --- a/tests/mag_complete_metadata_fixed_study.nf.test.snap +++ b/tests/mag_complete_metadata_fixed_study.nf.test.snap @@ -59,6 +59,19 @@ "multiqc/multiqc_data/multiqc_sample_registration.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf", + "multiqc/multiqc_plots/pdf/genome_metadata.pdf", + "multiqc/multiqc_plots/pdf/sample_registration.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/Genomes assigned accessions.png", + "multiqc/multiqc_plots/png/genome_metadata.png", + "multiqc/multiqc_plots/png/sample_registration.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/Genomes assigned accessions.svg", + "multiqc/multiqc_plots/svg/genome_metadata.svg", + "multiqc/multiqc_plots/svg/sample_registration.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" diff --git a/tests/mag_no_coverage_paired_reads.nf.test.snap b/tests/mag_no_coverage_paired_reads.nf.test.snap index ea4916bd..a3b68e51 100644 --- a/tests/mag_no_coverage_paired_reads.nf.test.snap +++ b/tests/mag_no_coverage_paired_reads.nf.test.snap @@ -67,6 +67,19 @@ "multiqc/multiqc_data/multiqc_sample_registration.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf", + "multiqc/multiqc_plots/pdf/genome_metadata.pdf", + "multiqc/multiqc_plots/pdf/sample_registration.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/Genomes assigned accessions.png", + "multiqc/multiqc_plots/png/genome_metadata.png", + "multiqc/multiqc_plots/png/sample_registration.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/Genomes assigned accessions.svg", + "multiqc/multiqc_plots/svg/genome_metadata.svg", + "multiqc/multiqc_plots/svg/sample_registration.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" diff --git a/tests/mag_no_coverage_single_reads.nf.test.snap b/tests/mag_no_coverage_single_reads.nf.test.snap index f2008f6a..f56b7274 100644 --- a/tests/mag_no_coverage_single_reads.nf.test.snap +++ b/tests/mag_no_coverage_single_reads.nf.test.snap @@ -67,6 +67,19 @@ "multiqc/multiqc_data/multiqc_sample_registration.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf", + "multiqc/multiqc_plots/pdf/genome_metadata.pdf", + "multiqc/multiqc_plots/pdf/sample_registration.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/Genomes assigned accessions.png", + "multiqc/multiqc_plots/png/genome_metadata.png", + "multiqc/multiqc_plots/png/sample_registration.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/Genomes assigned accessions.svg", + "multiqc/multiqc_plots/svg/genome_metadata.svg", + "multiqc/multiqc_plots/svg/sample_registration.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" diff --git a/tests/mag_no_taxonomy.nf.test.snap b/tests/mag_no_taxonomy.nf.test.snap index fc5cc526..725912d2 100644 --- a/tests/mag_no_taxonomy.nf.test.snap +++ b/tests/mag_no_taxonomy.nf.test.snap @@ -77,6 +77,19 @@ "multiqc/multiqc_data/multiqc_sample_registration.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf", + "multiqc/multiqc_plots/pdf/genome_metadata.pdf", + "multiqc/multiqc_plots/pdf/sample_registration.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/Genomes assigned accessions.png", + "multiqc/multiqc_plots/png/genome_metadata.png", + "multiqc/multiqc_plots/png/sample_registration.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/Genomes assigned accessions.svg", + "multiqc/multiqc_plots/svg/genome_metadata.svg", + "multiqc/multiqc_plots/svg/sample_registration.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" From c5301db42eb9424d3caea7a418e81356bec3d84f Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 14:54:13 +0100 Subject: [PATCH 10/18] Remove obsolete test_mag_no_study_complete_metadata snapshot Co-Authored-By: Claude Opus 5.5 --- tests/mag_complete_metadata.nf.test.snap | 96 +----------------------- 1 file changed, 2 insertions(+), 94 deletions(-) diff --git a/tests/mag_complete_metadata.nf.test.snap b/tests/mag_complete_metadata.nf.test.snap index 1a8dd07d..db109eff 100644 --- a/tests/mag_complete_metadata.nf.test.snap +++ b/tests/mag_complete_metadata.nf.test.snap @@ -85,102 +85,10 @@ "multiqc_genome_metadata.txt:md5,4364c96b13eb232b290c9f29b0edcf5a" ] ], - "timestamp": "2026-10-16T15:45:00.14863", + "timestamp": "2026-10-19T13:46:10.420328", "meta": { "nf-test": "0.9.5", - "nextflow": "26.10.0" - } - }, - "-profile test_mag_no_study_complete_metadata": { - "content": [ - 8, - { - "CONCAT_ACCESSIONS": { - "coreutils": 9.4, - "find": "4.6.0", - "pigz": 2.8 - }, - "CONCAT_METADATA": { - "coreutils": 9.4, - "find": "4.6.0", - "pigz": 2.8 - }, - "CREATE_GENOME_METADATA_TSV": { - "bash": "5.2.37(1)-release" - }, - "CREATE_MANIFESTS": { - "genome_uploader": "3.0.4" - }, - "FALINT": { - "falint": "1.2.0" - }, - "REGISTERSTUDY": { - "mgnify-pipelines-toolkit": "1.5.1" - }, - "SUBMIT": { - "ena-webin-cli": "9.0.3", - "mgnify-pipelines-toolkit": "1.5.1", - "python": "3.12.13" - }, - "Workflow": { - "nf-core/seqsubmit": "v1.0.0" - } - }, - [ - "mags", - "mags/complete_metadata", - "mags/complete_metadata/upload", - "mags/complete_metadata/upload/webin_cli", - "mags/complete_metadata/upload/webin_cli/complete_metadata_accessions.tsv", - "mags/upload", - "mags/upload/genomes_accessions.tsv", - "mags/upload/genomes_metadata.tsv", - "mags/upload/manifests", - "mags/upload/manifests/results", - "mags/upload/manifests/results/MAG_upload", - "mags/upload/manifests/results/MAG_upload/ENA_backup.json", - "mags/upload/manifests/results/MAG_upload/genome_samples.xml", - "mags/upload/manifests/results/MAG_upload/manifests_test", - "mags/upload/manifests/results/MAG_upload/registered_MAGs_test.tsv", - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_data/llms-full.txt", - "multiqc/multiqc_data/multiqc.log", - "multiqc/multiqc_data/multiqc.parquet", - "multiqc/multiqc_data/multiqc_Genomes assigned accessions.txt", - "multiqc/multiqc_data/multiqc_citations.txt", - "multiqc/multiqc_data/multiqc_data.json", - "multiqc/multiqc_data/multiqc_genome_metadata.txt", - "multiqc/multiqc_data/multiqc_sample_registration.txt", - "multiqc/multiqc_data/multiqc_software_versions.txt", - "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/Genomes assigned accessions.pdf", - "multiqc/multiqc_plots/pdf/genome_metadata.pdf", - "multiqc/multiqc_plots/pdf/sample_registration.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/Genomes assigned accessions.png", - "multiqc/multiqc_plots/png/genome_metadata.png", - "multiqc/multiqc_plots/png/sample_registration.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/Genomes assigned accessions.svg", - "multiqc/multiqc_plots/svg/genome_metadata.svg", - "multiqc/multiqc_plots/svg/sample_registration.svg", - "multiqc/multiqc_report.html", - "pipeline_info", - "pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml" - ], - [ - "genomes_metadata.tsv:md5,ae2b884015d1850fa63365e8a64d9fc8", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_genome_metadata.txt:md5,4364c96b13eb232b290c9f29b0edcf5a" - ] - ], - "timestamp": "2026-06-24T19:28:10.097952", - "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.0" + "nextflow": "26.04.1" } } } \ No newline at end of file From 3ffd6a5a4ba1c3cbcdb1ae0352ad614b4b39709a Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 14:59:25 +0100 Subject: [PATCH 11/18] explicitly set test_upload = true for tests, lint --- conf/test.config | 2 +- conf/test_assembly_complete_metadata.config | 2 +- conf/test_assembly_complete_metadata_fixed_study.config | 3 ++- conf/test_assembly_no_coverage_paired_reads.config | 1 + conf/test_assembly_no_coverage_single_reads.config | 1 + conf/test_assembly_one_contig.config | 1 + conf/test_full.config | 1 + conf/test_mag_complete_metadata.config | 2 +- conf/test_mag_complete_metadata_fixed_study.conf | 2 +- conf/test_mag_no_coverage_paired_reads.conf | 2 +- conf/test_mag_no_coverage_single_reads.conf | 2 +- conf/test_mag_no_quality.conf | 2 +- conf/test_mag_no_rna_presence.conf | 2 +- conf/test_mag_no_taxonomy.conf | 2 +- conf/test_mag_one_contig.conf | 2 +- 15 files changed, 16 insertions(+), 11 deletions(-) diff --git a/conf/test.config b/conf/test.config index 8f561785..9e10b02b 100644 --- a/conf/test.config +++ b/conf/test.config @@ -24,6 +24,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_multiple_bins_missing_metadata.csv' + outdir = 'test_output' mode = "mags" submission_study = "PRJEB98843" @@ -33,5 +34,4 @@ params { cat_db = params.pipelines_testdata_base_path + 'seqsubmit/test_data/small_cat_db/tax-db.tar.gz' checkm2_db = null - } diff --git a/conf/test_assembly_complete_metadata.config b/conf/test_assembly_complete_metadata.config index ac83a223..615e871b 100644 --- a/conf/test_assembly_complete_metadata.config +++ b/conf/test_assembly_complete_metadata.config @@ -24,6 +24,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/assembly_complete_metadata.csv' + outdir = 'test_output' mode = "metagenomic_assemblies" submission_study = null @@ -31,5 +32,4 @@ params { centre_name = "TEST_CENTER" test_upload = true - } diff --git a/conf/test_assembly_complete_metadata_fixed_study.config b/conf/test_assembly_complete_metadata_fixed_study.config index 801cab7b..2859de49 100644 --- a/conf/test_assembly_complete_metadata_fixed_study.config +++ b/conf/test_assembly_complete_metadata_fixed_study.config @@ -20,7 +20,7 @@ process { params { config_profile_name = 'Test --mode metagenomic_assemblies complete_metadata profile' - config_profile_description = 'Tests single assembly submission with all metadata provided in the samplesheet so the pipeline skips coverage calculation and only performs the upload to ENA. Submits to a pre-existing ENA study passed via --submission_study.' + config_profile_description = 'Tests single assembly submission with all metadata provided in the samplesheet so the pipeline skips coverage calculation and only performs the upload to ENA. Submits to a pre-existing ENA study passed via --submission_study.' // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/assembly_complete_metadata.csv' @@ -30,4 +30,5 @@ params { submission_study = "PRJEB98843" centre_name = "TEST_CENTER" + test_upload = true } diff --git a/conf/test_assembly_no_coverage_paired_reads.config b/conf/test_assembly_no_coverage_paired_reads.config index d933641b..4afb1d82 100644 --- a/conf/test_assembly_no_coverage_paired_reads.config +++ b/conf/test_assembly_no_coverage_paired_reads.config @@ -31,4 +31,5 @@ params { study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" + test_upload = true } diff --git a/conf/test_assembly_no_coverage_single_reads.config b/conf/test_assembly_no_coverage_single_reads.config index cffc4ce8..de9e064e 100644 --- a/conf/test_assembly_no_coverage_single_reads.config +++ b/conf/test_assembly_no_coverage_single_reads.config @@ -31,4 +31,5 @@ params { study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" + test_upload = true } diff --git a/conf/test_assembly_one_contig.config b/conf/test_assembly_one_contig.config index e2bc2700..fcb7bc7f 100644 --- a/conf/test_assembly_one_contig.config +++ b/conf/test_assembly_one_contig.config @@ -31,4 +31,5 @@ params { study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" + test_upload = true } diff --git a/conf/test_full.config b/conf/test_full.config index 16f6b49c..b7278aa6 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -16,6 +16,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_multiple_bins_missing_metadata.csv' + outdir = 'test_output' mode = "mags" submission_study = null diff --git a/conf/test_mag_complete_metadata.config b/conf/test_mag_complete_metadata.config index f316016b..4a1689e5 100644 --- a/conf/test_mag_complete_metadata.config +++ b/conf/test_mag_complete_metadata.config @@ -24,6 +24,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_complete_metadata.csv' + outdir = 'test_output' mode = "mags" submission_study = null @@ -34,5 +35,4 @@ params { cat_db = null checkm2_db = null - } diff --git a/conf/test_mag_complete_metadata_fixed_study.conf b/conf/test_mag_complete_metadata_fixed_study.conf index 428878a3..5fab85af 100644 --- a/conf/test_mag_complete_metadata_fixed_study.conf +++ b/conf/test_mag_complete_metadata_fixed_study.conf @@ -24,6 +24,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_complete_metadata.csv' + outdir = 'test_output' mode = "mags" submission_study = "PRJEB98843" @@ -33,5 +34,4 @@ params { cat_db = null checkm2_db = null - } diff --git a/conf/test_mag_no_coverage_paired_reads.conf b/conf/test_mag_no_coverage_paired_reads.conf index 50420200..920e9263 100644 --- a/conf/test_mag_no_coverage_paired_reads.conf +++ b/conf/test_mag_no_coverage_paired_reads.conf @@ -24,6 +24,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_coverage_paired_reads.csv' + outdir = 'test_output' mode = "mags" submission_study = null @@ -34,5 +35,4 @@ params { cat_db = null checkm2_db = null - } diff --git a/conf/test_mag_no_coverage_single_reads.conf b/conf/test_mag_no_coverage_single_reads.conf index 07feea47..ebbc5ce3 100644 --- a/conf/test_mag_no_coverage_single_reads.conf +++ b/conf/test_mag_no_coverage_single_reads.conf @@ -24,6 +24,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_coverage_single_reads.csv' + outdir = 'test_output' mode = "mags" submission_study = null @@ -34,5 +35,4 @@ params { cat_db = null checkm2_db = null - } diff --git a/conf/test_mag_no_quality.conf b/conf/test_mag_no_quality.conf index b396a521..4b8e12ce 100644 --- a/conf/test_mag_no_quality.conf +++ b/conf/test_mag_no_quality.conf @@ -24,6 +24,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_quality.csv' + outdir = 'test_output' mode = "mags" submission_study = null @@ -37,5 +38,4 @@ params { // which is not ideal but necessary to test the pipeline's behaviour with missing quality values // Track upstream issue here: https://github.com/chklovski/CheckM2/issues/140 checkm2_db = null - } diff --git a/conf/test_mag_no_rna_presence.conf b/conf/test_mag_no_rna_presence.conf index 18d489d1..d9d29909 100644 --- a/conf/test_mag_no_rna_presence.conf +++ b/conf/test_mag_no_rna_presence.conf @@ -24,6 +24,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_rna_presence.csv' + outdir = 'test_output' mode = "mags" submission_study = null @@ -34,5 +35,4 @@ params { cat_db = null checkm2_db = null - } diff --git a/conf/test_mag_no_taxonomy.conf b/conf/test_mag_no_taxonomy.conf index fbb373cb..3fea8048 100644 --- a/conf/test_mag_no_taxonomy.conf +++ b/conf/test_mag_no_taxonomy.conf @@ -24,6 +24,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_taxonomy.csv' + outdir = 'test_output' mode = "mags" submission_study = null @@ -34,5 +35,4 @@ params { cat_db = params.pipelines_testdata_base_path + 'seqsubmit/test_data/small_cat_db/tax-db.tar.gz' checkm2_db = null - } diff --git a/conf/test_mag_one_contig.conf b/conf/test_mag_one_contig.conf index 336eb776..06ec0ec1 100644 --- a/conf/test_mag_one_contig.conf +++ b/conf/test_mag_one_contig.conf @@ -24,6 +24,7 @@ params { // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_one_contig.csv' + outdir = 'test_output' mode = "mags" submission_study = null @@ -34,5 +35,4 @@ params { cat_db = null checkm2_db = null - } From 7064df377cfa23feba99ea18331c34a8a06bec6f Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 15:22:16 +0100 Subject: [PATCH 12/18] add random suffix to resolve study aliases clashing on CI --- bin/submit_study.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bin/submit_study.py b/bin/submit_study.py index 6c8b0d49..5c9a7ffa 100755 --- a/bin/submit_study.py +++ b/bin/submit_study.py @@ -13,6 +13,7 @@ import logging import os import sys +import uuid import xml.etree.ElementTree as ET from io import BytesIO from pathlib import Path @@ -327,7 +328,8 @@ def build_submission_xml( # SUBMISSION_SET submission_set = ET.SubElement(webin, "SUBMISSION_SET") submission = ET.SubElement(submission_set, "SUBMISSION") - sub_alias = f"study-submission-{datetime.datetime.now().strftime('%Y%m%d-%H%M%S')}" + # Random suffix keeps aliases unique when several submissions start in the same second + sub_alias = f"study-submission-{datetime.datetime.now().strftime('%Y%m%d-%H%M%S')}-{uuid.uuid4().hex[:4]}" submission.set("alias", sub_alias) actions = ET.SubElement(submission, "ACTIONS") main_action = ET.SubElement(actions, "ACTION") From b9351c64c7d206e84b54fcb767bd258cdf00bc9b Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 15:23:35 +0100 Subject: [PATCH 13/18] update test descriptions --- conf/test.config | 3 ++- conf/test_assembly_complete_metadata_fixed_study.config | 2 +- conf/test_mag_complete_metadata_fixed_study.conf | 2 +- conf/test_reads_paired.config | 3 ++- tests/assembly_complete_metadata_fixed_study.nf.test | 2 +- tests/mag_complete_metadata_fixed_study.nf.test | 2 +- tests/reads_paired_end.nf.test.snap | 9 ++++++--- 7 files changed, 14 insertions(+), 9 deletions(-) diff --git a/conf/test.config b/conf/test.config index 9e10b02b..93347675 100644 --- a/conf/test.config +++ b/conf/test.config @@ -27,7 +27,8 @@ params { outdir = 'test_output' mode = "mags" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" test_upload = true diff --git a/conf/test_assembly_complete_metadata_fixed_study.config b/conf/test_assembly_complete_metadata_fixed_study.config index 2859de49..f526e9fe 100644 --- a/conf/test_assembly_complete_metadata_fixed_study.config +++ b/conf/test_assembly_complete_metadata_fixed_study.config @@ -20,7 +20,7 @@ process { params { config_profile_name = 'Test --mode metagenomic_assemblies complete_metadata profile' - config_profile_description = 'Tests single assembly submission with all metadata provided in the samplesheet so the pipeline skips coverage calculation and only performs the upload to ENA. Submits to a pre-existing ENA study passed via --submission_study.' + config_profile_description = 'Tests single assembly submission with all metadata provided in the samplesheet so the pipeline skips coverage calculation and only performs the upload to ENA. Submits to a pre-existing ENA study passed via --submission_study, so requires maintainer Webin credentials with access to PRJEB98843.' // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/assembly_complete_metadata.csv' diff --git a/conf/test_mag_complete_metadata_fixed_study.conf b/conf/test_mag_complete_metadata_fixed_study.conf index 5fab85af..edfba5a8 100644 --- a/conf/test_mag_complete_metadata_fixed_study.conf +++ b/conf/test_mag_complete_metadata_fixed_study.conf @@ -20,7 +20,7 @@ process { params { config_profile_name = 'Test --mode mags complete_metadata profile' - config_profile_description = 'Tests single MAG submission with all metadata provided in the samplesheet, so the pipeline skips statistics and taxonomy calculation and only performs the upload to ENA. Submits to a pre-existing ENA study passed via --submission_study.' + config_profile_description = 'Tests single MAG submission with all metadata provided in the samplesheet, so the pipeline skips statistics and taxonomy calculation and only performs the upload to ENA. Submits to a pre-existing ENA study passed via --submission_study, so requires maintainer Webin credentials with access to PRJEB98843.' // Input data input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_complete_metadata.csv' diff --git a/conf/test_reads_paired.config b/conf/test_reads_paired.config index dc0ba4df..d4bbd084 100644 --- a/conf/test_reads_paired.config +++ b/conf/test_reads_paired.config @@ -27,7 +27,8 @@ params { outdir = 'test_output' mode = "reads" - submission_study = "PRJEB98843" + submission_study = null + study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json' centre_name = "TEST_CENTER" test_upload = true diff --git a/tests/assembly_complete_metadata_fixed_study.nf.test b/tests/assembly_complete_metadata_fixed_study.nf.test index 46215ce7..4b277a2c 100644 --- a/tests/assembly_complete_metadata_fixed_study.nf.test +++ b/tests/assembly_complete_metadata_fixed_study.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test assembly submission workflow - complete_metadata" + name "Test assembly submission workflow - complete_metadata (submission to existing study)" script "../main.nf" tag "pipeline" tag "mode_assembly" diff --git a/tests/mag_complete_metadata_fixed_study.nf.test b/tests/mag_complete_metadata_fixed_study.nf.test index 484e1fbe..a1392acd 100644 --- a/tests/mag_complete_metadata_fixed_study.nf.test +++ b/tests/mag_complete_metadata_fixed_study.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test genome submission workflow - complete_metadata" + name "Test genome submission workflow - complete_metadata (submission to existing study)" script "../main.nf" tag "pipeline" tag "mode_mag" diff --git a/tests/reads_paired_end.nf.test.snap b/tests/reads_paired_end.nf.test.snap index d4c288e5..7df80d1f 100644 --- a/tests/reads_paired_end.nf.test.snap +++ b/tests/reads_paired_end.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_reads_paired": { "content": [ - 4, + 5, { "CONCAT_ACCESSIONS": { "coreutils": 9.4, @@ -10,7 +10,10 @@ }, "CREATE_READS_MANIFEST": { "mgnify-pipelines-toolkit": "1.5.1" - }, + }, + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "SUBMIT": { "ena-webin-cli": "9.0.3", "mgnify-pipelines-toolkit": "1.5.1", @@ -45,7 +48,7 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-06-04T12:21:08.055365", + "timestamp": "2026-10-19T15:18:28.953324", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" From 8c03e38a8592fc5232d8f02a86356019c7eaa02d Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 15:24:15 +0100 Subject: [PATCH 14/18] update CONTRIBUTING.md --- docs/CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index f7dcfe1c..c07ae772 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -230,7 +230,7 @@ All submissions are performed via [Webin-CLI](https://github.com/enasequence/web ### Testing Requirements -All new functionality must be covered by tests. Running nf-tests that perform ENA submission locally requires ENA webin credentials. Contributors may ask for testing credentials on the nf-core Slack [#seqsubmit](https://nfcore.slack.com/channels/seqsubmit) channel. +All new functionality must be covered by tests. Running nf-tests that perform ENA submission locally requires ENA Webin credentials. Most tests register a new study, so any free [Webin account](https://www.ebi.ac.uk/ena/submit/webin/login) is enough. Only the `*_fixed_study` tests submit to the existing study `PRJEB98843` and need maintainer credentials; contributors may ask for them on the nf-core Slack [#seqsubmit](https://nfcore.slack.com/channels/seqsubmit) channel. At minimum, include: From 599994f2be23e337e22dae0a1987cdb88147bf82 Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 15:39:51 +0100 Subject: [PATCH 15/18] add trigger to only register study if at least one genome passed validation --- tests/assembly_one_contig.nf.test.snap | 9 +++------ tests/default.nf.test.snap | 13 ++++++++----- tests/mag_one_contig.nf.test.snap | 9 +++------ workflows/assemblysubmit.nf | 3 ++- workflows/genomesubmit.nf | 3 ++- 5 files changed, 18 insertions(+), 19 deletions(-) diff --git a/tests/assembly_one_contig.nf.test.snap b/tests/assembly_one_contig.nf.test.snap index 2d7c491e..491bbdf3 100644 --- a/tests/assembly_one_contig.nf.test.snap +++ b/tests/assembly_one_contig.nf.test.snap @@ -1,11 +1,8 @@ { "-profile test_assembly_one_contig": { "content": [ - 2, + 1, { - "REGISTERSTUDY": { - "mgnify-pipelines-toolkit": "1.5.1" - }, "Workflow": { "nf-core/seqsubmit": "v1.0.0" } @@ -31,10 +28,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-10-15T16:17:10.488596", + "timestamp": "2026-10-19T15:29:09.134422", "meta": { "nf-test": "0.9.5", - "nextflow": "26.10.0" + "nextflow": "26.04.1" } } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 4aadca31..10072b0f 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test": { "content": [ - 21, + 22, { "BARRNAP": { "barrnap": 0.9 @@ -40,6 +40,9 @@ "FALINT": { "falint": "1.2.0" }, + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "RENAME_FASTA_FOR_CATPACK": { "bash": "5.2.37(1)-release" }, @@ -131,10 +134,10 @@ "multiqc_genome_metadata.txt:md5,2f42824e9296d918b7f944037c27c717" ] ], + "timestamp": "2026-10-19T15:27:49.508151", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.0" - }, - "timestamp": "2026-06-24T15:59:38.733125" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } } } \ No newline at end of file diff --git a/tests/mag_one_contig.nf.test.snap b/tests/mag_one_contig.nf.test.snap index b3cb0c02..be530c2e 100644 --- a/tests/mag_one_contig.nf.test.snap +++ b/tests/mag_one_contig.nf.test.snap @@ -1,11 +1,8 @@ { "-profile test_mag_one_contig": { "content": [ - 2, + 1, { - "REGISTERSTUDY": { - "mgnify-pipelines-toolkit": "1.5.1" - }, "Workflow": { "nf-core/seqsubmit": "v1.0.0" } @@ -31,10 +28,10 @@ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], - "timestamp": "2026-10-15T16:19:46.817973", + "timestamp": "2026-10-19T15:29:21.389607", "meta": { "nf-test": "0.9.5", - "nextflow": "26.10.0" + "nextflow": "26.04.1" } } } \ No newline at end of file diff --git a/workflows/assemblysubmit.nf b/workflows/assemblysubmit.nf index 90273abd..bb3fe00f 100644 --- a/workflows/assemblysubmit.nf +++ b/workflows/assemblysubmit.nf @@ -136,7 +136,8 @@ workflow ASSEMBLYSUBMIT { } else { // Register a new study using the study metadata file REGISTERSTUDY( - channel.of([[id: "study"], file(study_metadata)]), + // Only register a study when at least one assembly passed validation + FASTA_VALIDATION.out.valid_fastas.first().map { _it -> [[id: "study"], file(study_metadata)] }, test_upload, release_date ) diff --git a/workflows/genomesubmit.nf b/workflows/genomesubmit.nf index 83f2cee6..17edbf94 100644 --- a/workflows/genomesubmit.nf +++ b/workflows/genomesubmit.nf @@ -226,7 +226,8 @@ workflow GENOMESUBMIT { study_accession_ch = channel.of(submission_study) } else { REGISTERSTUDY( - channel.of([[id: "study"], file(study_metadata)]), + // Only register a study when at least one genome passed validation + FASTA_VALIDATION.out.valid_fastas.first().map { _it -> [[id: "study"], file(study_metadata)] }, test_upload, release_date ) From 0765d4e538f75cfdcfc9028b912cfed899f4d00f Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 15:42:36 +0100 Subject: [PATCH 16/18] update CHANGELOG.md --- CHANGELOG.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c2e9b240..0ed0db0b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,9 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#116](https://github.com/nf-core/seqsubmit/pull/116) + - Most tests now register a new submission study, so they can be run with any Webin account. Only the `*_fixed_study` tests submit to the existing study `PRJEB98843` + - `test_upload = true` is set explicitly in all test configs + - Study submission alias now has a random suffix, so parallel registrations started in the same second no longer collide + - `REGISTERSTUDY` now runs only when at least one input passed validation ([#113](https://github.com/nf-core/seqsubmit/issues/113)) - [#106](https://github.com/nf-core/seqsubmit/pull/106) - Added support for metatranscriptome submission for ASSEMBLYSUBMIT - - Set retry to assembly_uploader + - Set retry to GENERATE_ASSEMBLY_MANIFEST module - [#108](https://github.com/nf-core/seqsubmit/pull/108) - Added test usecase in test-datasets https://github.com/nf-core/test-datasets/pull/2324 with contamination=0 - [#107](https://github.com/nf-core/seqsubmit/pull/107) From 1bef7e2548571c14fc4f38acec709852612fd675 Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Mon, 19 Oct 2026 16:11:31 +0100 Subject: [PATCH 17/18] update snapshot for test_mag_no_rna_presence --- tests/mag_no_rna_presence.nf.test.snap | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/tests/mag_no_rna_presence.nf.test.snap b/tests/mag_no_rna_presence.nf.test.snap index 7fec9d9f..e6349e8b 100644 --- a/tests/mag_no_rna_presence.nf.test.snap +++ b/tests/mag_no_rna_presence.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_mag_no_rna_presence": { "content": [ - 10, + 11, { "BARRNAP": { "barrnap": 0.9 @@ -28,6 +28,9 @@ "FALINT": { "falint": "1.2.0" }, + "REGISTERSTUDY": { + "mgnify-pipelines-toolkit": "1.5.1" + }, "SUBMIT": { "ena-webin-cli": "9.0.3", "mgnify-pipelines-toolkit": "1.5.1", @@ -100,10 +103,10 @@ "multiqc_genome_metadata.txt:md5,efa903988140642f4f3d12b8e034e7a1" ] ], + "timestamp": "2026-10-19T15:57:54.825156", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.0" - }, - "timestamp": "2026-06-24T16:13:51.780521" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } } } \ No newline at end of file From 4e39ced0a8a5f82aa2b69db81055f2bc28e7e25f Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Tue, 20 Oct 2026 15:18:59 +0100 Subject: [PATCH 18/18] rename *_fixed_study tests to *_existing_study --- CHANGELOG.md | 2 +- ...y_complete_metadata_existing_study.config} | 0 ...mag_complete_metadata_existing_study.conf} | 0 docs/CONTRIBUTING.md | 2 +- nextflow.config | 32 +++++++++---------- ..._complete_metadata_existing_study.nf.test} | 6 ++-- ...lete_metadata_existing_study.nf.test.snap} | 2 +- ..._complete_metadata_existing_study.nf.test} | 6 ++-- ...lete_metadata_existing_study.nf.test.snap} | 2 +- 9 files changed, 26 insertions(+), 26 deletions(-) rename conf/{test_assembly_complete_metadata_fixed_study.config => test_assembly_complete_metadata_existing_study.config} (100%) rename conf/{test_mag_complete_metadata_fixed_study.conf => test_mag_complete_metadata_existing_study.conf} (100%) rename tests/{assembly_complete_metadata_fixed_study.nf.test => assembly_complete_metadata_existing_study.nf.test} (88%) rename tests/{assembly_complete_metadata_fixed_study.nf.test.snap => assembly_complete_metadata_existing_study.nf.test.snap} (98%) rename tests/{mag_complete_metadata_fixed_study.nf.test => mag_complete_metadata_existing_study.nf.test} (89%) rename tests/{mag_complete_metadata_fixed_study.nf.test.snap => mag_complete_metadata_existing_study.nf.test.snap} (98%) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0ed0db0b..33b9d142 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - [#116](https://github.com/nf-core/seqsubmit/pull/116) - - Most tests now register a new submission study, so they can be run with any Webin account. Only the `*_fixed_study` tests submit to the existing study `PRJEB98843` + - All tests except the `*_existing_study` ones now register a new submission study, so they can be run with any Webin account ([#95](https://github.com/nf-core/seqsubmit/issues/95)). The `test_mag_complete_metadata_existing_study` and `test_assembly_complete_metadata_existing_study` tests submit to the existing study `PRJEB98843` and require maintainer Webin credentials - `test_upload = true` is set explicitly in all test configs - Study submission alias now has a random suffix, so parallel registrations started in the same second no longer collide - `REGISTERSTUDY` now runs only when at least one input passed validation ([#113](https://github.com/nf-core/seqsubmit/issues/113)) diff --git a/conf/test_assembly_complete_metadata_fixed_study.config b/conf/test_assembly_complete_metadata_existing_study.config similarity index 100% rename from conf/test_assembly_complete_metadata_fixed_study.config rename to conf/test_assembly_complete_metadata_existing_study.config diff --git a/conf/test_mag_complete_metadata_fixed_study.conf b/conf/test_mag_complete_metadata_existing_study.conf similarity index 100% rename from conf/test_mag_complete_metadata_fixed_study.conf rename to conf/test_mag_complete_metadata_existing_study.conf diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index c07ae772..ef3539bb 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -230,7 +230,7 @@ All submissions are performed via [Webin-CLI](https://github.com/enasequence/web ### Testing Requirements -All new functionality must be covered by tests. Running nf-tests that perform ENA submission locally requires ENA Webin credentials. Most tests register a new study, so any free [Webin account](https://www.ebi.ac.uk/ena/submit/webin/login) is enough. Only the `*_fixed_study` tests submit to the existing study `PRJEB98843` and need maintainer credentials; contributors may ask for them on the nf-core Slack [#seqsubmit](https://nfcore.slack.com/channels/seqsubmit) channel. +All new functionality must be covered by tests. Running nf-tests that perform ENA submission locally requires ENA Webin credentials. Tests that register a new study can be run with any free [Webin account](https://www.ebi.ac.uk/ena/submit/webin/login); this is every test except the `*_existing_study` ones. The `*_existing_study` tests submit to the existing study `PRJEB98843` and need maintainer credentials, which contributors may ask for on the nf-core Slack [#seqsubmit](https://nfcore.slack.com/channels/seqsubmit) channel. At minimum, include: diff --git a/nextflow.config b/nextflow.config index e420a539..9bddb0bb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -239,22 +239,22 @@ profiles { apptainer.runOptions = '--nv' singularity.runOptions = '--nv' } - test { includeConfig 'conf/test.config' } - test_full { includeConfig 'conf/test_full.config' } - test_mag_complete_metadata_fixed_study { includeConfig 'conf/test_mag_complete_metadata_fixed_study.conf' } - test_mag_complete_metadata { includeConfig 'conf/test_mag_complete_metadata.config' } - test_mag_no_coverage_single_reads { includeConfig 'conf/test_mag_no_coverage_single_reads.conf' } - test_mag_no_coverage_paired_reads { includeConfig 'conf/test_mag_no_coverage_paired_reads.conf' } - test_mag_no_quality { includeConfig 'conf/test_mag_no_quality.conf' } - test_mag_one_contig { includeConfig 'conf/test_mag_one_contig.conf' } - test_mag_no_rna_presence { includeConfig 'conf/test_mag_no_rna_presence.conf' } - test_mag_no_taxonomy { includeConfig 'conf/test_mag_no_taxonomy.conf' } - test_assembly_complete_metadata_fixed_study { includeConfig 'conf/test_assembly_complete_metadata_fixed_study.config' } - test_assembly_complete_metadata { includeConfig 'conf/test_assembly_complete_metadata.config' } - test_assembly_no_coverage_single_reads { includeConfig 'conf/test_assembly_no_coverage_single_reads.config' } - test_assembly_no_coverage_paired_reads { includeConfig 'conf/test_assembly_no_coverage_paired_reads.config' } - test_assembly_one_contig { includeConfig 'conf/test_assembly_one_contig.config' } - test_reads_paired { includeConfig 'conf/test_reads_paired.config' } + test { includeConfig 'conf/test.config' } + test_full { includeConfig 'conf/test_full.config' } + test_mag_complete_metadata_existing_study { includeConfig 'conf/test_mag_complete_metadata_existing_study.conf' } + test_mag_complete_metadata { includeConfig 'conf/test_mag_complete_metadata.config' } + test_mag_no_coverage_single_reads { includeConfig 'conf/test_mag_no_coverage_single_reads.conf' } + test_mag_no_coverage_paired_reads { includeConfig 'conf/test_mag_no_coverage_paired_reads.conf' } + test_mag_no_quality { includeConfig 'conf/test_mag_no_quality.conf' } + test_mag_one_contig { includeConfig 'conf/test_mag_one_contig.conf' } + test_mag_no_rna_presence { includeConfig 'conf/test_mag_no_rna_presence.conf' } + test_mag_no_taxonomy { includeConfig 'conf/test_mag_no_taxonomy.conf' } + test_assembly_complete_metadata_existing_study { includeConfig 'conf/test_assembly_complete_metadata_existing_study.config' } + test_assembly_complete_metadata { includeConfig 'conf/test_assembly_complete_metadata.config' } + test_assembly_no_coverage_single_reads { includeConfig 'conf/test_assembly_no_coverage_single_reads.config' } + test_assembly_no_coverage_paired_reads { includeConfig 'conf/test_assembly_no_coverage_paired_reads.config' } + test_assembly_one_contig { includeConfig 'conf/test_assembly_one_contig.config' } + test_reads_paired { includeConfig 'conf/test_reads_paired.config' } } // Load nf-core custom profiles from different institutions diff --git a/tests/assembly_complete_metadata_fixed_study.nf.test b/tests/assembly_complete_metadata_existing_study.nf.test similarity index 88% rename from tests/assembly_complete_metadata_fixed_study.nf.test rename to tests/assembly_complete_metadata_existing_study.nf.test index 4b277a2c..b289247f 100644 --- a/tests/assembly_complete_metadata_fixed_study.nf.test +++ b/tests/assembly_complete_metadata_existing_study.nf.test @@ -4,10 +4,10 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "mode_assembly" - tag "test_assembly_complete_metadata_fixed_study" - profile "test_assembly_complete_metadata_fixed_study" + tag "test_assembly_complete_metadata_existing_study" + profile "test_assembly_complete_metadata_existing_study" - test("-profile test_assembly_complete_metadata_fixed_study") { + test("-profile test_assembly_complete_metadata_existing_study") { when { params { diff --git a/tests/assembly_complete_metadata_fixed_study.nf.test.snap b/tests/assembly_complete_metadata_existing_study.nf.test.snap similarity index 98% rename from tests/assembly_complete_metadata_fixed_study.nf.test.snap rename to tests/assembly_complete_metadata_existing_study.nf.test.snap index ce607e8a..b2fd1c78 100644 --- a/tests/assembly_complete_metadata_fixed_study.nf.test.snap +++ b/tests/assembly_complete_metadata_existing_study.nf.test.snap @@ -1,5 +1,5 @@ { - "-profile test_assembly_complete_metadata_fixed_study": { + "-profile test_assembly_complete_metadata_existing_study": { "content": [ 7, { diff --git a/tests/mag_complete_metadata_fixed_study.nf.test b/tests/mag_complete_metadata_existing_study.nf.test similarity index 89% rename from tests/mag_complete_metadata_fixed_study.nf.test rename to tests/mag_complete_metadata_existing_study.nf.test index a1392acd..1dc5e0f4 100644 --- a/tests/mag_complete_metadata_fixed_study.nf.test +++ b/tests/mag_complete_metadata_existing_study.nf.test @@ -4,10 +4,10 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "mode_mag" - tag "test_mag_complete_metadata_fixed_study" - profile "test_mag_complete_metadata_fixed_study" + tag "test_mag_complete_metadata_existing_study" + profile "test_mag_complete_metadata_existing_study" - test("-profile test_mag_complete_metadata_fixed_study") { + test("-profile test_mag_complete_metadata_existing_study") { when { params { diff --git a/tests/mag_complete_metadata_fixed_study.nf.test.snap b/tests/mag_complete_metadata_existing_study.nf.test.snap similarity index 98% rename from tests/mag_complete_metadata_fixed_study.nf.test.snap rename to tests/mag_complete_metadata_existing_study.nf.test.snap index 5786f91e..39b86531 100644 --- a/tests/mag_complete_metadata_fixed_study.nf.test.snap +++ b/tests/mag_complete_metadata_existing_study.nf.test.snap @@ -1,5 +1,5 @@ { - "-profile test_mag_complete_metadata_fixed_study": { + "-profile test_mag_complete_metadata_existing_study": { "content": [ 7, {