From 02acd44caf5ba6e764ed3cd509506e9eccc18b63 Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 11:13:27 +0200 Subject: [PATCH 1/6] 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 2793fd64..095a27c0 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": "2026-05-13T13:17:16.523674" + "nf-test": "0.9.5", + "nextflow": "26.10.0" + } } } \ No newline at end of file From 3ee526ffdc8c47100b29194ad360075744fac53b Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 12:12:28 +0200 Subject: [PATCH 2/6] 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 533388e2..9d622434 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": "1.3.5" }, + "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": "2026-05-13T13:18:47.77148" + "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 67ccc9b6..cf61cb2d 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": "1.3.5" }, + "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": "2026-05-13T13:19:25.904346" + "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 cc7c484cbd9081f6529133732c243d29355eb477 Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 12:14:19 +0200 Subject: [PATCH 3/6] 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 a8be583ffb14c94bf2a9e7d80b670d13d4129d18 Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 15:20:28 +0200 Subject: [PATCH 4/6] 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 601c9f4a8db8dbb0c392dccb8800cfe9cfec78ba Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 15:36:51 +0200 Subject: [PATCH 5/6] 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 a24634f57f1c75e914564482db1472b833cff81d Mon Sep 17 00:00:00 2001 From: Ann Loraine Date: Fri, 16 Oct 2026 15:46:37 +0200 Subject: [PATCH 6/6] 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