diff --git a/bin/get_eatlas_accessions.py b/bin/get_eatlas_accessions.py index 58f72443..2b8b2dde 100755 --- a/bin/get_eatlas_accessions.py +++ b/bin/get_eatlas_accessions.py @@ -108,7 +108,7 @@ def get_data(url: str) -> dict: return response.json() -def get_experiment_description(exp_dict: dict): +def get_experiment_description(exp_dict: dict) -> str: """ Gets the description from an experiment dictionary @@ -138,7 +138,7 @@ def get_experiment_description(exp_dict: dict): raise KeyError(f"Could not find description field in {exp_dict}") -def get_experiment_accession(exp_dict: dict): +def get_experiment_accession(exp_dict: dict) -> str: """ Gets the accession from an experiment dictionary @@ -168,7 +168,7 @@ def get_experiment_accession(exp_dict: dict): raise KeyError(f"Could not find accession field in {exp_dict}") -def get_properties_values(exp_dict: dict): +def get_properties_values(exp_dict: dict) -> list: """ Gets all values from properties from an experiment dictionary @@ -199,7 +199,7 @@ def get_properties_values(exp_dict: dict): return list(set(values)) -def get_eatlas_experiments(): +def get_eatlas_experiments() -> list[dict]: """ Gets all experiments from Expression Atlas @@ -215,7 +215,7 @@ def get_eatlas_experiments(): return data["experiments"] -def filter_by_platform(experiments: list[dict], platform: str | None): +def filter_by_platform(experiments: list[dict], platform: str | None) -> list[dict]: """ Gets all experiments for a given platform from Expression Atlas Possible platforms in Expression Atlas are 'rnaseq', 'microarray', 'proteomics' @@ -258,7 +258,15 @@ def filter_by_platform(experiments: list[dict], platform: str | None): return platform_experiments -def get_species_experiments(experiments: list[dict], species: str): +def get_species_name_without_subspecies(species: str) -> str: + """ + Returns the species name without the subspecies part. + Ex: Hordeum vulgare subsp. vulgare -> Hordeum vulgare + """ + return " ".join(species.split(" ")[:2]) + + +def get_species_experiments(experiments: list[dict], species: str) -> list[dict]: """ Gets all experiments for a given species from Expression Atlas @@ -275,12 +283,14 @@ def get_species_experiments(experiments: list[dict], species: str): """ species_experiments = [] for exp_dict in experiments: - if exp_dict["species"] == species: + # in case the species name contains a subspecies part, we only use the first two words + exp_species = get_species_name_without_subspecies(exp_dict["species"]) + if exp_species == species: species_experiments.append(exp_dict) return species_experiments -def get_experiment_data(exp_dict: dict): +def get_experiment_data(exp_dict: dict) -> dict: """ Gets the full data for an experiment given its dictionary @@ -312,7 +322,7 @@ def filter_out_excluded_accessions(experiments: list[dict]) -> list[dict]: return valid_experiments -def parse_experiment(exp_dict: dict): +def parse_experiment(exp_dict: dict) -> dict: # getting accession and description accession = get_experiment_accession(exp_dict) description = get_experiment_description(exp_dict) diff --git a/conf/test.config b/conf/test.config index fdf68236..dc27bed9 100644 --- a/conf/test.config +++ b/conf/test.config @@ -16,6 +16,6 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Input data - species = 'beta vulgaris' + species = 'prunus persica' outdir = "results/test" } diff --git a/galaxy/build/static/template.xml b/galaxy/build/static/template.xml index d10fd6fc..d8035286 100644 --- a/galaxy/build/static/template.xml +++ b/galaxy/build/static/template.xml @@ -109,7 +109,7 @@ INPUTS
- + @@ -128,7 +128,7 @@ INPUTS
- + diff --git a/galaxy/tool_shed/tool/nf_core_stableexpression.xml b/galaxy/tool_shed/tool/nf_core_stableexpression.xml index 57d81dd3..27ccaa5e 100644 --- a/galaxy/tool_shed/tool/nf_core_stableexpression.xml +++ b/galaxy/tool_shed/tool/nf_core_stableexpression.xml @@ -586,7 +586,7 @@ VERSION="1.1dev"; echo "$VERSION"
- + @@ -605,7 +605,7 @@ VERSION="1.1dev"; echo "$VERSION"
- + diff --git a/subworkflows/local/download_public_datasets/main.nf b/subworkflows/local/download_public_datasets/main.nf index 6ea3f11f..9e6d2a2f 100644 --- a/subworkflows/local/download_public_datasets/main.nf +++ b/subworkflows/local/download_public_datasets/main.nf @@ -1,4 +1,4 @@ -include { EXPRESSIONATLAS_GETDATA as EXPRESSION_ATLAS } from '../../../modules/local/expressionatlas/getdata' +include { EXPRESSIONATLAS_GETDATA as EXPRESSION_ATLAS } from '../../../modules/local/expressionatlas/getdata' include { GEO_GETDATA as GEO } from '../../../modules/local/geo/getdata' include { addDatasetIdToMetadata } from '../utils_nfcore_stableexpression_pipeline' @@ -7,7 +7,7 @@ include { augmentMetadata } from '../utils_nfcore_ /* ======================================================================================== - SUBWORKFLOW TO DOWNLOAD GEO ACCESSIONS AND DATASETS + SUBWORKFLOW TO DOWNLOAD EXPRESSION ATLAS AND NCBI GEO DATASETS ======================================================================================== */ diff --git a/subworkflows/local/gene_statistics/main.nf b/subworkflows/local/gene_statistics/main.nf index bfb924b9..3237e7dd 100644 --- a/subworkflows/local/gene_statistics/main.nf +++ b/subworkflows/local/gene_statistics/main.nf @@ -1,9 +1,9 @@ -include { COMPUTE_GENE_STATISTICS as GLOBAL } from '../../../modules/local/compute_gene_statistics' -include { COMPUTE_GENE_STATISTICS as PLATFORM } from '../../../modules/local/compute_gene_statistics' +include { COMPUTE_GENE_STATISTICS as GLOBAL } from '../../../modules/local/compute_gene_statistics' +include { COMPUTE_GENE_STATISTICS as PLATFORM } from '../../../modules/local/compute_gene_statistics' /* ======================================================================================== - SUBWORKFLOW TO DOWNLOAD EXPRESSIONATLAS ACCESSIONS AND DATASETS + SUBWORKFLOW TO COMPUTE STATISTICS FOR ALL GENES ======================================================================================== */ diff --git a/subworkflows/local/genorm/main.nf b/subworkflows/local/genorm/main.nf index c491566f..6a88703e 100644 --- a/subworkflows/local/genorm/main.nf +++ b/subworkflows/local/genorm/main.nf @@ -16,7 +16,7 @@ include { COMPUTE_M_MEASURE } from '../../../modules/local/genorm/com /* ======================================================================================== - SUBWORKFLOW TO COMPUTE PAIRWISE GENE VARIATION + SUBWORKFLOW TO COMPUTE PAIRWISE GENE VARIATION (ADAPTED VERSION OF GENORM) ======================================================================================== */ diff --git a/subworkflows/local/get_public_accessions/main.nf b/subworkflows/local/get_public_accessions/main.nf index debb29e0..73558f6d 100644 --- a/subworkflows/local/get_public_accessions/main.nf +++ b/subworkflows/local/get_public_accessions/main.nf @@ -3,7 +3,7 @@ include { GEO_GETACCESSIONS as GEO } from '../ /* ======================================================================================== - SUBWORKFLOW TO DOWNLOAD EXPRESSIONATLAS ACCESSIONS AND DATASETS + SUBWORKFLOW TO FETCH EXPRESSION ATLAS AND NCBI GEO ACCESSIONS ======================================================================================== */ diff --git a/subworkflows/local/get_transcript_lengths/main.nf b/subworkflows/local/get_transcript_lengths/main.nf index 26213245..df54de83 100644 --- a/subworkflows/local/get_transcript_lengths/main.nf +++ b/subworkflows/local/get_transcript_lengths/main.nf @@ -4,7 +4,7 @@ include { DOWNLOAD_ENSEMBL_ANNOTATION } from '../../../modules/ /* ======================================================================================== - SUBWORKFLOW TO DOWNLOAD EXPRESSIONATLAS ACCESSIONS AND DATASETS + SUBWORKFLOW TO GET TRANSCRIPT LENGTHS FROM GENOME ANNOTATION ======================================================================================== */ diff --git a/subworkflows/local/idmapping/main.nf b/subworkflows/local/idmapping/main.nf index 489f97dd..5bf16957 100644 --- a/subworkflows/local/idmapping/main.nf +++ b/subworkflows/local/idmapping/main.nf @@ -7,7 +7,7 @@ include { FILTER_AND_RENAME_GENES } from '../../../modules/local/ /* ======================================================================================== - SUBWORKFLOW TO DOWNLOAD EXPRESSIONATLAS ACCESSIONS AND DATASETS + SUBWORKFLOW TO MAP GENE IDS TO COMMON IDS AMONG ALL DATASETS AND TO REMOVE RARE GENES ======================================================================================== */ diff --git a/subworkflows/local/merge_data/main.nf b/subworkflows/local/merge_data/main.nf index a093c8f5..55b6cc52 100644 --- a/subworkflows/local/merge_data/main.nf +++ b/subworkflows/local/merge_data/main.nf @@ -50,7 +50,7 @@ workflow MERGE_DATA { .collect( sort: true ) .map { files -> [ [ platform: "all" ], files ] } - GLOBAL( ch_collected_merged_counts.collect() ) + GLOBAL( ch_collected_merged_counts ) ch_all_counts = GLOBAL.out.counts // ----------------------------------------------------------------- diff --git a/subworkflows/local/reporting/main.nf b/subworkflows/local/reporting/main.nf index 0c560204..9d4fa676 100644 --- a/subworkflows/local/reporting/main.nf +++ b/subworkflows/local/reporting/main.nf @@ -11,7 +11,7 @@ include { paramsSummaryMap } from 'plugin/nf-schema' /* ======================================================================================== - SUBWORKFLOW TO DOWNLOAD EXPRESSIONATLAS ACCESSIONS AND DATASETS + SUBWORKFLOW DEDICATED TO AGGREGATION OF RESULTS AND REPORTING (DASH APP AND MULTIQC) ======================================================================================== */ diff --git a/subworkflows/local/sample_filtering/main.nf b/subworkflows/local/sample_filtering/main.nf index 06ac9cec..31006f3f 100644 --- a/subworkflows/local/sample_filtering/main.nf +++ b/subworkflows/local/sample_filtering/main.nf @@ -1,5 +1,5 @@ -include { FILTER_OUT_SAMPLES_WITH_TOO_MANY_ZEROS as TOO_MANY_ZEROS } from '../../../modules/local/filter_out_samples/with_too_many_zeros' -include { FILTER_OUT_SAMPLES_WITH_TOO_MANY_MISSING_VALUES as TOO_MANY_MISSING_VALUES } from '../../../modules/local/filter_out_samples/with_too_many_missing_values' +include { FILTER_OUT_SAMPLES_WITH_TOO_MANY_ZEROS as TOO_MANY_ZEROS } from '../../../modules/local/filter_out_samples/with_too_many_zeros' +include { FILTER_OUT_SAMPLES_WITH_TOO_MANY_MISSING_VALUES as TOO_MANY_MISSING_VALUES } from '../../../modules/local/filter_out_samples/with_too_many_missing_values' /* diff --git a/subworkflows/local/stability_scoring/main.nf b/subworkflows/local/stability_scoring/main.nf index 3f731949..d6a2de39 100644 --- a/subworkflows/local/stability_scoring/main.nf +++ b/subworkflows/local/stability_scoring/main.nf @@ -6,7 +6,7 @@ include { GENORM } from '../genorm' /* ======================================================================================== - COMPUTE STABILITY SCORES + SUBWORKFLOW TO COMPUTE STABILITY SCORES ======================================================================================== */ @@ -61,7 +61,7 @@ workflow STABILITY_SCORING { // ----------------------------------------------------------------- // AGGREGATION AND FINAL STABILITY SCORE // ----------------------------------------------------------------- - //ch_normfinder_stabilities.join( ch_genorm_stability ).join( ch_section_stats ), + COMPUTE_STABILITY_SCORES ( ch_normfinder_stabilities.join( ch_genorm_stability ).join( ch_section_stats ), stability_score_weights diff --git a/tests/default.nf.test b/tests/default.nf.test index 908fb62b..58102a53 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - species = 'beta vulgaris' + species = 'prunus persica' outdir = "$outputDir" } } @@ -110,7 +110,7 @@ nextflow_pipeline { when { params { - species = 'beta vulgaris' + species = 'arabidopsis lyrata' accessions_only = true outdir = "$outputDir" } @@ -140,7 +140,7 @@ nextflow_pipeline { when { params { - species = 'beta vulgaris' + species = 'aspergillus fumigatus' download_only = true outdir = "$outputDir" } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index aad13d07..87571ee3 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -419,356 +419,11 @@ "renaming_warning_reasons.tsv:md5,0a11a59b5b547a39ab7a0e4dac622173" ] ], - "timestamp": "2026-04-05T09:10:44.402386214", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" - } - }, - "-profile test_fetch_geo": { - "content": [ - [ - "aggregated", - "aggregated/all_genes_summary.csv", - "aggregated/custom_content_multiqc_config.yaml", - "aggregated/section_1.most_stable_genes_summary.csv", - "aggregated/section_1.most_stable_genes_transposed_counts.csv", - "aggregated/section_10.most_stable_genes_summary.csv", - "aggregated/section_10.most_stable_genes_transposed_counts.csv", - "aggregated/section_11.most_stable_genes_summary.csv", - "aggregated/section_11.most_stable_genes_transposed_counts.csv", - "aggregated/section_12.most_stable_genes_summary.csv", - "aggregated/section_12.most_stable_genes_transposed_counts.csv", - "aggregated/section_13.most_stable_genes_summary.csv", - "aggregated/section_13.most_stable_genes_transposed_counts.csv", - "aggregated/section_14.most_stable_genes_summary.csv", - "aggregated/section_14.most_stable_genes_transposed_counts.csv", - "aggregated/section_15.most_stable_genes_summary.csv", - "aggregated/section_15.most_stable_genes_transposed_counts.csv", - "aggregated/section_16.most_stable_genes_summary.csv", - "aggregated/section_16.most_stable_genes_transposed_counts.csv", - "aggregated/section_17.most_stable_genes_summary.csv", - "aggregated/section_17.most_stable_genes_transposed_counts.csv", - "aggregated/section_18.most_stable_genes_summary.csv", - "aggregated/section_18.most_stable_genes_transposed_counts.csv", - "aggregated/section_19.most_stable_genes_summary.csv", - "aggregated/section_19.most_stable_genes_transposed_counts.csv", - "aggregated/section_2.most_stable_genes_summary.csv", - "aggregated/section_2.most_stable_genes_transposed_counts.csv", - "aggregated/section_20.most_stable_genes_summary.csv", - "aggregated/section_20.most_stable_genes_transposed_counts.csv", - "aggregated/section_3.most_stable_genes_summary.csv", - "aggregated/section_3.most_stable_genes_transposed_counts.csv", - "aggregated/section_4.most_stable_genes_summary.csv", - "aggregated/section_4.most_stable_genes_transposed_counts.csv", - "aggregated/section_5.most_stable_genes_summary.csv", - "aggregated/section_5.most_stable_genes_transposed_counts.csv", - "aggregated/section_6.most_stable_genes_summary.csv", - "aggregated/section_6.most_stable_genes_transposed_counts.csv", - "aggregated/section_7.most_stable_genes_summary.csv", - "aggregated/section_7.most_stable_genes_transposed_counts.csv", - "aggregated/section_8.most_stable_genes_summary.csv", - "aggregated/section_8.most_stable_genes_transposed_counts.csv", - "aggregated/section_9.most_stable_genes_summary.csv", - "aggregated/section_9.most_stable_genes_transposed_counts.csv", - "dash_app", - "dash_app/app.py", - "dash_app/assets", - "dash_app/assets/style.css", - "dash_app/data", - "dash_app/data/all_counts.imputed.parquet", - "dash_app/data/all_genes_summary.csv", - "dash_app/data/whole_design.csv", - "dash_app/environment.yml", - "dash_app/src", - "dash_app/src/callbacks", - "dash_app/src/callbacks/common.py", - "dash_app/src/callbacks/genes.py", - "dash_app/src/callbacks/samples.py", - "dash_app/src/components", - "dash_app/src/components/graphs.py", - "dash_app/src/components/icons.py", - "dash_app/src/components/right_sidebar.py", - "dash_app/src/components/settings", - "dash_app/src/components/settings/genes.py", - "dash_app/src/components/settings/samples.py", - "dash_app/src/components/stores.py", - "dash_app/src/components/tables.py", - "dash_app/src/components/tooltips.py", - "dash_app/src/components/top.py", - "dash_app/src/utils", - "dash_app/src/utils/config.py", - "dash_app/src/utils/data_management.py", - "dash_app/src/utils/style.py", - "errors", - "gene_length", - "gene_length/Beta_vulgaris.RefBeet-1.2.2.62.gff3.gz", - "gene_length/gene_transcript_lengths.csv", - "geo", - "idmapping", - "idmapping/global_gene_id_mapping.csv", - "idmapping/global_gene_metadata.csv", - "idmapping/gprofiler", - "idmapping/gprofiler/gene_metadata.csv", - "idmapping/gprofiler/mapped_gene_ids.csv", - "idmapping/renamed", - "idmapping/renamed/E_MTAB_8187_rnaseq.rnaseq.raw.counts.cleaned.renamed.parquet", - "idmapping/renamed/GSE55951_GPL18429.microarray.normalised.counts.cleaned.renamed.parquet", - "merged_datasets", - "merged_datasets/whole_design.csv", - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_data/llms-full.txt", - "multiqc/multiqc_data/multiqc.log", - "multiqc/multiqc_data/multiqc.parquet", - "multiqc/multiqc_data/multiqc_citations.txt", - "multiqc/multiqc_data/multiqc_data.json", - "multiqc/multiqc_data/multiqc_eatlas_all_experiments_metadata.txt", - "multiqc/multiqc_data/multiqc_eatlas_selected_experiments_metadata.txt", - "multiqc/multiqc_data/multiqc_gene_statistics.txt", - "multiqc/multiqc_data/multiqc_genes_section_1.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_1.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_10.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_11.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_12.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_13.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_14.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_15.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_16.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_17.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_18.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_19.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_2.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_3.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_4.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_5.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_6.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_7.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_8.txt", - "multiqc/multiqc_data/multiqc_genes_section_1_9.txt", - "multiqc/multiqc_data/multiqc_geo_all_experiments_metadata.txt", - "multiqc/multiqc_data/multiqc_geo_rejected_experiments_metadata.txt", - "multiqc/multiqc_data/multiqc_geo_selected_experiments_metadata.txt", - "multiqc/multiqc_data/multiqc_geo_warning_reasons.txt", - "multiqc/multiqc_data/multiqc_id_mapping_stats.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_1.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_10.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_11.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_12.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_13.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_14.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_15.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_16.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_17.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_18.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_19.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_2.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_3.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_4.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_5.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_6.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_7.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_8.txt", - "multiqc/multiqc_data/multiqc_normalised_expr_distrib_section_1_9.txt", - "multiqc/multiqc_data/multiqc_null_values_filter.txt", - "multiqc/multiqc_data/multiqc_ratio_nulls.txt", - "multiqc/multiqc_data/multiqc_ratio_zeros.txt", - "multiqc/multiqc_data/multiqc_renaming_warning_reasons.txt", - "multiqc/multiqc_data/multiqc_skewness.txt", - "multiqc/multiqc_data/multiqc_software_versions.txt", - "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_data/multiqc_total_gene_id_occurrence_quantiles.txt", - "multiqc/multiqc_data/multiqc_zero_values_filter.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/genes_section_1.pdf", - "multiqc/multiqc_plots/pdf/normalised_expr_distrib_section_1.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/genes_section_1.png", - "multiqc/multiqc_plots/png/normalised_expr_distrib_section_1.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/genes_section_1.svg", - "multiqc/multiqc_plots/svg/normalised_expr_distrib_section_1.svg", - "multiqc/multiqc_report.html", - "normalised", - "normalised/quantile_normalised", - "normalised/quantile_normalised/E_MTAB_8187_rnaseq", - "normalised/quantile_normalised/E_MTAB_8187_rnaseq/E_MTAB_8187_rnaseq.rnaseq.raw.counts.cleaned.renamed.zeros_filtered.nulls_filtered.tpm.quant_norm.parquet", - "normalised/tpm", - "normalised/tpm/E_MTAB_8187_rnaseq", - "normalised/tpm/E_MTAB_8187_rnaseq/E_MTAB_8187_rnaseq.rnaseq.raw.counts.cleaned.renamed.zeros_filtered.nulls_filtered.tpm.parquet", - "pipeline_info", - "pipeline_info/nf_core_stableexpression_software_mqc_versions.yml", - "public_data", - 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"-profile test": { "content": [ @@ -962,7 +617,7 @@ "dash_app/src/utils/style.py", "errors", "gene_length", - "gene_length/Beta_vulgaris.RefBeet-1.2.2.62.gff3.gz", + "gene_length/Prunus_persica.Prunus_persica_NCBIv2.62.chr.gff3.gz", "gene_length/gene_transcript_lengths.csv", "idmapping", "idmapping/global_gene_id_mapping.csv", @@ -971,7 +626,7 @@ "idmapping/gprofiler/gene_metadata.csv", "idmapping/gprofiler/mapped_gene_ids.csv", "idmapping/renamed", - "idmapping/renamed/E_MTAB_8187_rnaseq.rnaseq.raw.counts.cleaned.renamed.parquet", + "idmapping/renamed/E_ENAD_3_rnaseq.rnaseq.raw.counts.cleaned.renamed.parquet", "merged_datasets", "merged_datasets/whole_design.csv", "multiqc", @@ -1046,11 +701,11 @@ "multiqc/multiqc_report.html", "normalised", "normalised/quantile_normalised", - "normalised/quantile_normalised/E_MTAB_8187_rnaseq", - 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"multiqc_null_values_filter.txt:md5,9f39dde761d2be72b989b3da51d9b768", + "multiqc_ratio_nulls.txt:md5,fd9acca0d6995183d30b6ef2489a596e", + "multiqc_ratio_zeros.txt:md5,7de1385d524ab670ffa9ddaf4cb8735b", + "multiqc_total_gene_id_occurrence_quantiles.txt:md5,4f5408fbf6cedc9160035dc0322781dd", + "multiqc_zero_values_filter.txt:md5,9f39dde761d2be72b989b3da51d9b768", + "accessions.txt:md5,c1a80aeb676be48beefb1df23a80da5b", + "selected_experiments.metadata.tsv:md5,f0f38d66449a88b9b95347d2d2ab4c68", + "species_experiments.metadata.tsv:md5,f0f38d66449a88b9b95347d2d2ab4c68", + "E_ENAD_3_rnaseq.design.csv:md5,376b9275a5b04892372bdecd1e51738d", + "E_ENAD_3_rnaseq.rnaseq.raw.counts.csv:md5,856b851cb139c3ddef5883efe2d85cfe", + "id_mapping_stats.csv:md5,574b7a35bd7fb4bb0122e5c7742d2b64", + "missing_values_filter_stats.csv:md5,a6fdf3c5250dc46a43f79a9ec5a1355d", + "ratio_nulls.csv:md5,f9d04a18f447dc5df3076cd3cebec755", + "ratio_nulls_per_sample.csv:md5,9606b597f36ab94930be607b2207c88b", + "ratio_zeros.csv:md5,72926e3905e83dd22a5a2dc62aa98d1d", + "zero_values_filter_stats.csv:md5,a6fdf3c5250dc46a43f79a9ec5a1355d" ] ], - "timestamp": "2026-04-05T09:07:09.566479758", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-16T11:45:04.163764784" }, "-profile test_accessions_only": { "content": [ @@ -1234,16 +889,16 @@ ], [ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "accessions.txt:md5,76e5e3af7c72eac7a1993a2bd75b4d1a", - "selected_experiments.metadata.tsv:md5,cf220f0d0aab141abf220c856430f2f2", - "species_experiments.metadata.tsv:md5,cf220f0d0aab141abf220c856430f2f2" + "accessions.txt:md5,b63b86661ce5d73c1c95436ebaf146a1", + "selected_experiments.metadata.tsv:md5,2af519969d9c77cc74d92723ee171c48", + "species_experiments.metadata.tsv:md5,2af519969d9c77cc74d92723ee171c48" ] ], - "timestamp": "2026-03-29T14:35:30.092884854", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-16T11:58:55.484363676" }, "-profile test_one_accession_low_gene_count": { "content": [ @@ -1672,11 +1327,11 @@ "zero_values_filter_stats.csv:md5,766d888e41179e8a785f634b3b606bc9" ] ], - "timestamp": "2026-04-05T09:30:42.794565916", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-05T09:30:42.794565916" }, "-profile test_public_and_dataset": { "content": [ @@ -1921,7 +1576,7 @@ "mapped_gene_ids.csv:md5,7eecbd2d88adaf5f213f238a72d28b99", "whole_design.csv:md5,fbd18d011d7d855452e5a30a303afcbf", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_eatlas_all_experiments_metadata.txt:md5,8b7643e0ef8eaaa3fa72f7103fd7ccee", + "multiqc_eatlas_all_experiments_metadata.txt:md5,6ea661253a55d41687e32fea72961063", "multiqc_eatlas_selected_experiments_metadata.txt:md5,8b7643e0ef8eaaa3fa72f7103fd7ccee", "multiqc_gene_statistics.txt:md5,d7750cb95663a63219dcec94e03d7af1", "multiqc_genes_section_1.txt:md5,f310a16068d5e76713497e2d3824cf2d", @@ -1972,7 +1627,7 @@ "multiqc_zero_values_filter.txt:md5,4082d32f92221ed686e79910c6d2f6b3", "accessions.txt:md5,76e5e3af7c72eac7a1993a2bd75b4d1a", "selected_experiments.metadata.tsv:md5,cf220f0d0aab141abf220c856430f2f2", - "species_experiments.metadata.tsv:md5,cf220f0d0aab141abf220c856430f2f2", + "species_experiments.metadata.tsv:md5,7c354b570fd393d913bdf1fc53db1db8", "E_MTAB_8187_rnaseq.design.csv:md5,fbd18d011d7d855452e5a30a303afcbf", "E_MTAB_8187_rnaseq.rnaseq.raw.counts.csv:md5,fe221fd94f66df7120b0590091e14eb1", "id_mapping_stats.csv:md5,dc2d9d7f34e570411c8cf5885b447719", @@ -1983,11 +1638,11 @@ "zero_values_filter_stats.csv:md5,17fc6d525450d34445bf9cc25defe18a" ] ], - "timestamp": "2026-04-05T09:16:48.007287186", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-16T11:58:29.889348049" }, "-profile test_download_only": { "content": [ @@ -2026,24 +1681,24 @@ "public_data/expression_atlas/accessions/selected_experiments.metadata.tsv", "public_data/expression_atlas/accessions/species_experiments.metadata.tsv", "public_data/expression_atlas/datasets", - "public_data/expression_atlas/datasets/E_MTAB_8187_rnaseq.design.csv", - "public_data/expression_atlas/datasets/E_MTAB_8187_rnaseq.rnaseq.raw.counts.csv", + "public_data/expression_atlas/datasets/E_MTAB_5309_rnaseq.design.csv", + "public_data/expression_atlas/datasets/E_MTAB_5309_rnaseq.rnaseq.raw.counts.csv", "statistics", "warnings" ], [ "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "accessions.txt:md5,76e5e3af7c72eac7a1993a2bd75b4d1a", - "selected_experiments.metadata.tsv:md5,cf220f0d0aab141abf220c856430f2f2", - "species_experiments.metadata.tsv:md5,cf220f0d0aab141abf220c856430f2f2", - "E_MTAB_8187_rnaseq.design.csv:md5,fbd18d011d7d855452e5a30a303afcbf", - "E_MTAB_8187_rnaseq.rnaseq.raw.counts.csv:md5,fe221fd94f66df7120b0590091e14eb1" + "accessions.txt:md5,f43aeb39de22137f546d2edf66d51228", + "selected_experiments.metadata.tsv:md5,d8254b794ee7a57ae6e31a72e8e2d822", + "species_experiments.metadata.tsv:md5,d8254b794ee7a57ae6e31a72e8e2d822", + "E_MTAB_5309_rnaseq.design.csv:md5,2556c1fd31b15eda7e4bbe042c83cc39", + "E_MTAB_5309_rnaseq.rnaseq.raw.counts.csv:md5,5c45a59ce7fbc59e5784f40dfb8c3b71" ] ], - "timestamp": "2026-03-29T14:36:07.351960504", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-16T11:59:27.717850311" } } \ No newline at end of file diff --git a/tests/modules/local/aggregate_results/main.nf.test.snap b/tests/modules/local/aggregate_results/main.nf.test.snap index ef6e609a..bfa2a9aa 100644 --- a/tests/modules/local/aggregate_results/main.nf.test.snap +++ b/tests/modules/local/aggregate_results/main.nf.test.snap @@ -61,11 +61,11 @@ ] } ], - "timestamp": "2026-04-04T09:38:02.365611798", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-04T09:38:02.365611798" }, "Without microarray": { "content": [ @@ -129,11 +129,11 @@ ] } ], - "timestamp": "2026-03-30T14:06:37.615799808", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T14:06:37.615799808" }, "One invalid target gene": { "content": [ @@ -197,11 +197,11 @@ ] } ], - "timestamp": "2026-03-30T14:47:07.501875225", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T14:47:07.501875225" }, "One section": { "content": [ @@ -253,11 +253,11 @@ ] } ], - "timestamp": "2026-03-30T14:47:13.474058057", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T14:47:13.474058057" }, "With microarray": { "content": [ @@ -321,10 +321,10 @@ ] } ], - "timestamp": "2026-03-30T14:46:55.231695582", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T14:46:55.231695582" } } \ No newline at end of file diff --git a/tests/modules/local/compute_gene_statistics/main.nf.test.snap b/tests/modules/local/compute_gene_statistics/main.nf.test.snap index 9db76e85..0e7756f2 100644 --- a/tests/modules/local/compute_gene_statistics/main.nf.test.snap +++ b/tests/modules/local/compute_gene_statistics/main.nf.test.snap @@ -24,11 +24,11 @@ ] } ], - "timestamp": "2026-03-30T14:48:46.011713833", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T14:48:46.011713833" }, "No platform": { "content": [ @@ -55,11 +55,11 @@ ] } ], - "timestamp": "2026-03-30T14:48:33.525954126", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T14:48:33.525954126" }, "RNAseq platform": { "content": [ @@ -86,10 +86,10 @@ ] } ], - "timestamp": "2026-03-30T14:48:39.77826003", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T14:48:39.77826003" } } \ No newline at end of file diff --git a/tests/modules/local/compute_stability_scores/main.nf.test.snap b/tests/modules/local/compute_stability_scores/main.nf.test.snap index ebedc0ce..5b386ca1 100644 --- a/tests/modules/local/compute_stability_scores/main.nf.test.snap +++ b/tests/modules/local/compute_stability_scores/main.nf.test.snap @@ -24,11 +24,11 @@ ] } ], - "timestamp": "2026-03-30T15:20:22.075756497", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T15:20:22.075756497" }, "Without Genorm": { "content": [ @@ -55,10 +55,10 @@ ] } ], - "timestamp": "2026-03-30T15:20:28.206402711", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T15:20:28.206402711" } } \ No newline at end of file diff --git a/tests/modules/local/expressionatlas/getaccessions/main.nf.test.snap b/tests/modules/local/expressionatlas/getaccessions/main.nf.test.snap index 01391db2..f784b39f 100644 --- a/tests/modules/local/expressionatlas/getaccessions/main.nf.test.snap +++ b/tests/modules/local/expressionatlas/getaccessions/main.nf.test.snap @@ -57,11 +57,11 @@ ] } ], - "timestamp": "2026-02-19T10:19:07.035607232", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-02-19T10:19:07.035607232" }, "Solanum tuberosum no keyword": { "content": [ @@ -121,10 +121,10 @@ ] } ], - "timestamp": "2026-02-19T10:19:20.628916067", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-02-19T10:19:20.628916067" } } \ No newline at end of file diff --git a/tests/modules/local/expressionatlas/getdata/main.nf.test.snap b/tests/modules/local/expressionatlas/getdata/main.nf.test.snap index 74bcd293..cc3b5be5 100644 --- a/tests/modules/local/expressionatlas/getdata/main.nf.test.snap +++ b/tests/modules/local/expressionatlas/getdata/main.nf.test.snap @@ -36,11 +36,11 @@ ] } ], - "timestamp": "2026-03-19T12:17:31.898448037", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-19T12:17:31.898448037" }, "Arabidopsis Geo dataset": { "content": [ @@ -79,11 +79,11 @@ ] } ], - "timestamp": "2026-03-29T16:45:22.368557567", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-29T16:45:22.368557567" }, "Transcription profiling by array of Arabidopsis mutant for fis2 (microarray)": { "content": [ @@ -122,10 +122,10 @@ ] } ], - "timestamp": "2026-03-19T12:17:45.546042421", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-19T12:17:45.546042421" } } \ No newline at end of file diff --git a/tests/modules/local/filter_and_rename_genes/main.nf.test.snap b/tests/modules/local/filter_and_rename_genes/main.nf.test.snap index 5c57a3d7..874f066c 100644 --- a/tests/modules/local/filter_and_rename_genes/main.nf.test.snap +++ b/tests/modules/local/filter_and_rename_genes/main.nf.test.snap @@ -42,11 +42,11 @@ ] } ], - "timestamp": "2026-04-02T15:03:17.972937783", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:04:45.840061804" }, "Map Ensembl IDs": { "content": [ @@ -98,11 +98,11 @@ ] } ], - "timestamp": "2026-04-02T15:03:06.767979138", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:04:26.849187591" }, "No valid gene": { "content": [ @@ -147,10 +147,10 @@ ] } ], - "timestamp": "2026-04-02T15:03:12.057594832", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:04:36.329611443" } } \ No newline at end of file diff --git a/tests/modules/local/genorm/compute_m_measure/main.nf.test.snap b/tests/modules/local/genorm/compute_m_measure/main.nf.test.snap index f8ea8893..767f3dd7 100644 --- a/tests/modules/local/genorm/compute_m_measure/main.nf.test.snap +++ b/tests/modules/local/genorm/compute_m_measure/main.nf.test.snap @@ -34,10 +34,10 @@ ] } ], - "timestamp": "2026-03-30T15:40:23.09370734", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T15:40:23.09370734" } } \ No newline at end of file diff --git a/tests/modules/local/genorm/cross_join/main.nf.test.snap b/tests/modules/local/genorm/cross_join/main.nf.test.snap index b11d3254..50d11bc4 100644 --- a/tests/modules/local/genorm/cross_join/main.nf.test.snap +++ b/tests/modules/local/genorm/cross_join/main.nf.test.snap @@ -38,10 +38,10 @@ ] } ], - "timestamp": "2026-03-30T15:40:29.248178717", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T15:40:29.248178717" } } \ No newline at end of file diff --git a/tests/modules/local/genorm/expression_ratio/main.nf.test.snap b/tests/modules/local/genorm/expression_ratio/main.nf.test.snap index f0347aba..a9e492ef 100644 --- a/tests/modules/local/genorm/expression_ratio/main.nf.test.snap +++ b/tests/modules/local/genorm/expression_ratio/main.nf.test.snap @@ -38,10 +38,10 @@ ] } ], - "timestamp": "2026-04-01T09:41:39.459415462", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-01T09:41:39.459415462" } } \ No newline at end of file diff --git a/tests/modules/local/genorm/make_chunks/main.nf.test.snap b/tests/modules/local/genorm/make_chunks/main.nf.test.snap index 6cb9d08f..5b2f00be 100644 --- a/tests/modules/local/genorm/make_chunks/main.nf.test.snap +++ b/tests/modules/local/genorm/make_chunks/main.nf.test.snap @@ -56,10 +56,10 @@ ] } ], - "timestamp": "2026-03-30T15:40:46.563584649", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T15:40:46.563584649" } } \ No newline at end of file diff --git a/tests/modules/local/genorm/ratio_standard_variation/main.nf.test.snap b/tests/modules/local/genorm/ratio_standard_variation/main.nf.test.snap index a16d5709..6f29543d 100644 --- a/tests/modules/local/genorm/ratio_standard_variation/main.nf.test.snap +++ b/tests/modules/local/genorm/ratio_standard_variation/main.nf.test.snap @@ -38,10 +38,10 @@ ] } ], - "timestamp": "2026-04-01T09:41:51.590963847", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-01T09:41:51.590963847" } } \ No newline at end of file diff --git a/tests/modules/local/get_candidate_genes/main.nf.test.snap b/tests/modules/local/get_candidate_genes/main.nf.test.snap index c9e2ede4..7b869fd2 100644 --- a/tests/modules/local/get_candidate_genes/main.nf.test.snap +++ b/tests/modules/local/get_candidate_genes/main.nf.test.snap @@ -46,11 +46,11 @@ ] } ], - "timestamp": "2026-03-30T17:07:03.292271274", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T17:07:03.292271274" }, "Too many sections": { "content": [ @@ -123,10 +123,10 @@ ] } ], - "timestamp": "2026-03-30T17:07:09.643611957", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T17:07:09.643611957" } } \ No newline at end of file diff --git a/tests/modules/local/gprofiler/idmapping/main.nf.test.snap b/tests/modules/local/gprofiler/idmapping/main.nf.test.snap index 33550d23..850dae54 100644 --- a/tests/modules/local/gprofiler/idmapping/main.nf.test.snap +++ b/tests/modules/local/gprofiler/idmapping/main.nf.test.snap @@ -34,10 +34,10 @@ ] } ], - "timestamp": "2026-02-19T10:26:01.249646558", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-02-19T10:26:01.249646558" } } \ No newline at end of file diff --git a/tests/modules/local/merge_counts/main.nf.test.snap b/tests/modules/local/merge_counts/main.nf.test.snap index 7290c51d..6e773d44 100644 --- a/tests/modules/local/merge_counts/main.nf.test.snap +++ b/tests/modules/local/merge_counts/main.nf.test.snap @@ -34,11 +34,11 @@ ] } ], - "timestamp": "2026-03-30T16:41:25.646239587", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T16:41:25.646239587" }, "3 files": { "content": [ @@ -75,10 +75,10 @@ ] } ], - "timestamp": "2026-03-30T16:39:46.447995126", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T16:39:46.447995126" } } \ No newline at end of file diff --git a/tests/modules/local/normalisation/compute_cpm/main.nf.test.snap b/tests/modules/local/normalisation/compute_cpm/main.nf.test.snap index 5bcd2643..6f3d7957 100644 --- a/tests/modules/local/normalisation/compute_cpm/main.nf.test.snap +++ b/tests/modules/local/normalisation/compute_cpm/main.nf.test.snap @@ -40,11 +40,11 @@ ] } ], - "timestamp": "2026-04-02T15:06:33.626810331", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:07:24.246785277" }, "One group": { "content": [ @@ -87,11 +87,11 @@ ] } ], - "timestamp": "2026-03-19T12:23:45.874853063", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-19T12:23:45.874853063" }, "TSV files": { "content": [ @@ -134,11 +134,11 @@ ] } ], - "timestamp": "2026-03-19T12:23:54.407797312", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-19T12:23:54.407797312" }, "Rows with many zeros": { "content": [ @@ -181,10 +181,10 @@ ] } ], - "timestamp": "2026-04-02T15:06:39.394957809", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:07:34.001566313" } } \ No newline at end of file diff --git a/tests/modules/local/normalisation/compute_tpm/main.nf.test.snap b/tests/modules/local/normalisation/compute_tpm/main.nf.test.snap index f150a846..287c19f0 100644 --- a/tests/modules/local/normalisation/compute_tpm/main.nf.test.snap +++ b/tests/modules/local/normalisation/compute_tpm/main.nf.test.snap @@ -40,11 +40,11 @@ ] } ], - "timestamp": "2026-04-02T15:06:57.587153369", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:08:02.882187442" }, "One group": { "content": [ @@ -87,11 +87,11 @@ ] } ], - "timestamp": "2026-04-02T15:07:10.080660208", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:08:21.950858405" }, "TSV files": { "content": [ @@ -134,11 +134,11 @@ ] } ], - "timestamp": "2026-04-02T15:07:16.231969197", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:08:31.427239077" }, "Rows with many zeros": { "content": [ @@ -181,10 +181,10 @@ ] } ], - "timestamp": "2026-04-02T15:07:03.89821637", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:08:12.502224484" } } \ No newline at end of file diff --git a/tests/modules/local/normfinder/main.nf.test.snap b/tests/modules/local/normfinder/main.nf.test.snap index 4e90417c..0b2298f7 100644 --- a/tests/modules/local/normfinder/main.nf.test.snap +++ b/tests/modules/local/normfinder/main.nf.test.snap @@ -55,11 +55,11 @@ ] } ], - "timestamp": "2026-03-30T15:45:00.995645591", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T15:45:00.995645591" }, "Very small dataset - Cq values": { "content": [ @@ -117,10 +117,10 @@ ] } ], - "timestamp": "2026-03-30T15:44:51.060894512", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-30T15:44:51.060894512" } } \ No newline at end of file diff --git a/tests/modules/local/quantile_normalisation/main.nf.test.snap b/tests/modules/local/quantile_normalisation/main.nf.test.snap index ef0a01eb..1e2bce1c 100644 --- a/tests/modules/local/quantile_normalisation/main.nf.test.snap +++ b/tests/modules/local/quantile_normalisation/main.nf.test.snap @@ -41,11 +41,11 @@ ] } ], - "timestamp": "2026-04-02T15:07:43.185701068", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:09:10.597987851" }, "Normal target distribution": { "content": [ @@ -89,10 +89,10 @@ ] } ], - "timestamp": "2026-04-02T15:07:51.53574005", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-17T09:09:22.718260106" } } \ No newline at end of file diff --git a/tests/subworkflows/local/download_public_datasets/main.nf.test.snap b/tests/subworkflows/local/download_public_datasets/main.nf.test.snap index f02a885b..3e299483 100644 --- a/tests/subworkflows/local/download_public_datasets/main.nf.test.snap +++ b/tests/subworkflows/local/download_public_datasets/main.nf.test.snap @@ -26,11 +26,11 @@ ] } ], - "timestamp": "2025-12-16T15:18:21.726044151", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - } + }, + "timestamp": "2025-12-16T15:18:21.726044151" }, "Beta vulgaris - Eatlas + GEO - all accessions": { "content": [ @@ -77,10 +77,10 @@ ] } ], - "timestamp": "2025-12-16T15:18:08.622422246", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - } + }, + "timestamp": "2025-12-16T15:18:08.622422246" } } \ No newline at end of file diff --git a/tests/subworkflows/local/expression_normalisation/main.nf.test.snap b/tests/subworkflows/local/expression_normalisation/main.nf.test.snap index 0b893abd..04a5c4ec 100644 --- a/tests/subworkflows/local/expression_normalisation/main.nf.test.snap +++ b/tests/subworkflows/local/expression_normalisation/main.nf.test.snap @@ -44,11 +44,11 @@ ] } ], - "timestamp": "2026-03-19T12:27:13.766132141", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-19T12:27:13.766132141" }, "No rnaseq normalisation": { "content": [ @@ -77,11 +77,11 @@ ] } ], - "timestamp": "2026-03-19T12:27:25.897836784", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-19T12:27:25.897836784" }, "TPM Normalisation with gene length": { "content": [ @@ -128,11 +128,11 @@ ] } ], - "timestamp": "2026-03-19T12:27:00.268510601", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-19T12:27:00.268510601" }, "TPM Normalisation": { "content": [ @@ -179,10 +179,10 @@ ] } ], - "timestamp": "2026-03-19T12:26:44.852023368", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-19T12:26:44.852023368" } } \ No newline at end of file diff --git a/tests/subworkflows/local/genorm/main.nf.test.snap b/tests/subworkflows/local/genorm/main.nf.test.snap index 813be1cf..411b8f60 100644 --- a/tests/subworkflows/local/genorm/main.nf.test.snap +++ b/tests/subworkflows/local/genorm/main.nf.test.snap @@ -20,11 +20,11 @@ ] } ], - "timestamp": "2026-04-01T09:56:47.48692894", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-01T09:56:47.48692894" }, "10 genes": { "content": [ @@ -47,10 +47,10 @@ ] } ], - "timestamp": "2026-04-01T09:55:53.207791305", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-01T09:55:53.207791305" } } \ No newline at end of file diff --git a/tests/subworkflows/local/get_public_accessions/main.nf.test.snap b/tests/subworkflows/local/get_public_accessions/main.nf.test.snap index ed1f7832..d19a70fb 100644 --- a/tests/subworkflows/local/get_public_accessions/main.nf.test.snap +++ b/tests/subworkflows/local/get_public_accessions/main.nf.test.snap @@ -3,12 +3,14 @@ "content": [ { "0": [ + "E-ENAD-2", "E-GEOD-61690", "E-MTAB-552", "E-MTAB-8187", "E-PROT-138" ], "accessions": [ + "E-ENAD-2", "E-GEOD-61690", "E-MTAB-552", "E-MTAB-8187", @@ -16,22 +18,24 @@ ] } ], - "timestamp": "2026-04-01T14:49:26.109506348", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-16T12:25:30.194867058" }, "No GEO + accessions provided": { "content": [ { "0": [ + "E-ENAD-2", "E-GEOD-61690", "E-MTAB-552", "E-MTAB-8187", "E-PROT-138" ], "accessions": [ + "E-ENAD-2", "E-GEOD-61690", "E-MTAB-552", "E-MTAB-8187", @@ -39,28 +43,30 @@ ] } ], - "timestamp": "2026-04-01T14:49:15.733265214", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-16T12:25:15.508377196" }, "Fetch eatlas accessions without keywords": { "content": [ { "0": [ + "E-ENAD-2", "E-MTAB-8187" ], "accessions": [ + "E-ENAD-2", "E-MTAB-8187" ] } ], - "timestamp": "2026-04-01T14:48:43.670211053", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-16T12:25:00.873486754" }, "With samplling size": { "content": [ @@ -73,37 +79,10 @@ ] } ], - "timestamp": "2026-04-01T14:53:02.05138484", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } - }, - "Fetch public accessions with keywords": { - "content": [ - { - "0": [ - "E-MTAB-8187", - "GSE107627", - "GSE114968", - "GSE269454", - "GSE281272", - "GSE79526" - ], - "accessions": [ - "E-MTAB-8187", - "GSE107627", - "GSE114968", - "GSE269454", - "GSE281272", - "GSE79526" - ] - } - ], - "timestamp": "2026-04-01T14:49:04.709620479", - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-01T14:53:02.05138484" } } \ No newline at end of file diff --git a/workflows/stableexpression.nf b/workflows/stableexpression.nf index 09325a3a..a823a320 100644 --- a/workflows/stableexpression.nf +++ b/workflows/stableexpression.nf @@ -36,14 +36,10 @@ workflow STABLEEXPRESSION { ch_all_counts = channel.empty() ch_all_imputed_counts = channel.empty() ch_whole_design = channel.empty() - ch_whole_design = channel.empty() ch_stats_all_genes_with_scores = channel.empty() ch_platform_statistics = channel.empty() ch_whole_gene_metadata = channel.empty() ch_whole_gene_id_mapping = channel.empty() - ch_most_stable_genes_summary = channel.empty() - ch_all_genes_statistics = channel.empty() - ch_most_stable_genes_transposed_counts = channel.empty() def species = params.species.split(' ').join('_').toLowerCase()