integration test

integration test #732

Manually triggered January 9, 2025 12:19

DriesSchaumont

⁠ beaa995

refactor_neighbors_leiden_umap

Status Success

Total duration 1h 18m 51s

Artifacts –

integration-test.yml

on: workflow_dispatch

build / Build and push target folder

6m 1s

sync_s3

2m 23s

Matrix: build / build_and_deploy_docker_containers

Matrix: integration_test

Annotations

156 warnings

sync_s3

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build / Build and push target folder

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build / bcl_convert - demux - Build and push docker image

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build / calculate_qc_metrics - qc - Build and push docker image

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build / add_id - metadata - Build and push docker image

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build / bcl2fastq - demux - Build and push docker image

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build / cellranger_atac_mkfastq - demux - Build and push docker image

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build / build_bdrhap_reference - reference - Build and push docker image

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build / build_cellranger_reference - reference - Build and push docker image

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build / binning - scgpt - Build and push docker image

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build / calculate_atac_qc_metrics - qc - Build and push docker image

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build / cellranger_atac_count - mapping - Build and push docker image

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build / build_cellranger_arc_reference - reference - Build and push docker image

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build / bcftools - genetic_demux - Build and push docker image

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build / bbknn - neighbors - Build and push docker image

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build / cellranger_count - mapping - Build and push docker image

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build / cellranger_mkfastq - demux - Build and push docker image

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build / bd_rhapsody - mapping - Build and push docker image

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build / cellranger_count_split - mapping - Build and push docker image

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build / compress_h5mu - compression - Build and push docker image

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build / cellranger_mkgtf - reference - Build and push docker image

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build / build_star_reference - reference - Build and push docker image

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build / delete_layer - transform - Build and push docker image

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build / clr - transform - Build and push docker image

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build / concatenate_h5mu - dataflow - Build and push docker image

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build / celltypist - annotate - Build and push docker image

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build / delimit_fraction - filter - Build and push docker image

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build / cellranger_multi - mapping - Build and push docker image

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build / densmap - dimred - Build and push docker image

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build / cellsnp - genetic_demux - Build and push docker image

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build / download_file - download - Build and push docker image

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build / duplicate_var - metadata - Build and push docker image

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build / cellxgene_census - query - Build and push docker image

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build / cellbender_remove_background_v0_2 - correction - Build and push docker image

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build / do_filter - filter - Build and push docker image

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build / freebayes - genetic_demux - Build and push docker image

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build / duplicate_obs - metadata - Build and push docker image

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build / filter_with_counts - filter - Build and push docker image

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build / fastqc - qc - Build and push docker image

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build / from_bd_to_10x_molecular_barcode_tags - convert - Build and push docker image

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build / filter_10xh5 - process_10xh5 - Build and push docker image

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build / from_h5mu_to_h5ad - convert - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / filter_with_scrublet - filter - Build and push docker image

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build / cell_type_annotation - scgpt - Build and push docker image

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build / from_bdrhap_to_h5mu - convert - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / from_h5ad_to_h5mu - convert - Build and push docker image

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build / from_10xmtx_to_h5mu - convert - Build and push docker image

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build / find_neighbors - neighbors - Build and push docker image

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build / dsc_pileup - genetic_demux - Build and push docker image

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build / grep_annotation_column - metadata - Build and push docker image

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build / from_cellranger_multi_to_h5mu - convert - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / htseq_count_to_h5mu - mapping - Build and push docker image

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build / join_csv - metadata - Build and push docker image

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build / harmonypy - integrate - Build and push docker image

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build / join_uns_to_obs - metadata - Build and push docker image

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build / from_h5mu_to_seurat - convert - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / from_10xh5_to_h5mu - convert - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / htseq_count - mapping - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / highly_variable_features_scanpy - feature_annotation - Build and push docker image

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build / intersect_obs - filter - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / cross_check_genes - scgpt - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / cellbender_remove_background - correction - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / make_params - files - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / knn - labels_transfer - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / bpcells_regress_out - transform - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / lsi - dimred - Build and push docker image

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build / move_obsm_to_obs - metadata - Build and push docker image

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build / move_layer - transform - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / make_reference - reference - Build and push docker image

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build / merge - dataflow - Build and push docker image

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build / leiden - cluster - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / multiqc - qc - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / multi_star_to_h5mu - mapping - Build and push docker image

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build / publish - transfer - Build and push docker image

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build / lianapy - interpret - Build and push docker image

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build / embedding - scgpt - Build and push docker image

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build / normalize_total - transform - Build and push docker image

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build / samtools_sort - mapping - Build and push docker image

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build / demuxlet - genetic_demux - Build and push docker image

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build / mermaid - report - Build and push docker image

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build / regress_out - transform - Build and push docker image

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build / log1p - transform - Build and push docker image

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build / remove_modality - filter - Build and push docker image

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build / random_forest_annotation - annotate - Build and push docker image

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build / freemuxlet - genetic_demux - Build and push docker image

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build / scanorama - integrate - Build and push docker image

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build / scale - transform - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / score_genes_cell_cycle_scanpy - feature_annotation - Build and push docker image

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build / pca - dimred - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / scsplit - genetic_demux - Build and push docker image

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build / split_h5mu - dataflow - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / souporcell - genetic_demux - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / scvelo - velocity - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / split_h5mu_train_test - dataflow - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / multi_star - mapping - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / samtools - genetic_demux - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / split_modalities - dataflow - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / score_genes_scanpy - feature_annotation - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / subset_h5mu - filter - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / svm_annotation - annotate - Build and push docker image

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build / subset_obsp - filter - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / tar_extract - compression - Build and push docker image

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build / tsne - dimred - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / pad_tokenize - scgpt - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / star_align_v273a - mapping - Build and push docker image

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build / umap - dimred - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / vireo - genetic_demux - Build and push docker image

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build / tfidf - transform - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / velocyto - velocity - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / velocyto_to_h5mu - convert - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / star_align - mapping - Build and push docker image

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build / xgboost - labels_transfer - Build and push docker image

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build / sync_test_resources - download - Build and push docker image

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build / onclass - annotate - Build and push docker image

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build / scanvi - annotate - Build and push docker image

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build / popv - annotate - Build and push docker image

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build / scarches - integrate - Build and push docker image

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build / scvi - integrate - Build and push docker image

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build / totalvi - integrate - Build and push docker image

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integration_test (gdo_singlesample, workflows/gdo, src/workflows/gdo/gdo_singlesample//test.nf, t...

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integration_test (bbknn_leiden, workflows/integration, src/workflows/integration/bbknn_leiden//te...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (conversion, workflows/ingestion, src/workflows/ingestion/conversion//test.nf, t...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (harmony_leiden, workflows/integration, src/workflows/integration/harmony_leiden...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (bbknn_leiden, workflows/integration, src/workflows/integration/bbknn_leiden//te...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (demux, workflows/ingestion, src/workflows/ingestion/demux//test.nf, test_wf, sr...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (cellranger_postprocessing, workflows/ingestion, src/workflows/ingestion/cellran...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (harmony_leiden, workflows/integration, src/workflows/integration/harmony_leiden...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (cellranger_mapping, workflows/ingestion, src/workflows/ingestion/cellranger_map...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (cellranger_multi, workflows/ingestion, src/workflows/ingestion/cellranger_multi...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (dimensionality_reduction, workflows/multiomics, src/workflows/multiomics/dimens...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (prot_singlesample, workflows/prot, src/workflows/prot/prot_singlesample//test.n...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (cellranger_multi, workflows/ingestion, src/workflows/ingestion/cellranger_multi...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (prot_multisample, workflows/prot, src/workflows/prot/prot_multisample//test.nf,...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (cellranger_postprocessing, workflows/ingestion, src/workflows/ingestion/cellran...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (qc, workflows/qc, src/workflows/qc/qc//test.nf, test_wf, src/workflows/qc/qc/co...

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integration_test (rna_singlesample, workflows/rna, src/workflows/rna/rna_singlesample//test.nf, t...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (rna_multisample, workflows/rna, src/workflows/rna/rna_multisample//test.nf, tes...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (rna_singlesample, workflows/rna, src/workflows/rna/rna_singlesample//test.nf, t...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (scanorama_leiden, workflows/integration, src/workflows/integration/scanorama_le...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (scanorama_leiden, workflows/integration, src/workflows/integration/scanorama_le...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (process_batches, workflows/multiomics, src/workflows/multiomics/process_batches...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (process_batches, workflows/multiomics, src/workflows/multiomics/process_batches...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (bd_rhapsody, workflows/ingestion, src/workflows/ingestion/bd_rhapsody//test.nf,...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (split_modalities, workflows/multiomics, src/workflows/multiomics/split_modaliti...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (make_reference, workflows/ingestion, src/workflows/ingestion/make_reference//te...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (scvi_leiden, workflows/integration, src/workflows/integration/scvi_leiden//test...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (scgpt_annotation, workflows/annotation, src/workflows/annotation/scgpt_annotati...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (totalvi_leiden, workflows/integration, src/workflows/integration/totalvi_leiden...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (scgpt_integration_knn, workflows/annotation, src/workflows/annotation/scgpt_int...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (scgpt_leiden, workflows/integration, src/workflows/integration/scgpt_leiden//te...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

integration_test (scgpt_leiden, workflows/integration, src/workflows/integration/scgpt_leiden//te...

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

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integration test #732

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integration test #732

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integration-test.yml

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