integration test #644

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Job	Run time
sync_s3	1m 55s
build / Build and push target folder	5m 52s
build / Build and Deploy Docker Images (celltypist, /, annotate, src/annotate/celltypist/config.vsh.yaml,...	3m 24s
build / Build and Deploy Docker Images (onclass, /, annotate, src/annotate/onclass/config.vsh.yaml, src/a...	11m 18s
build / Build and Deploy Docker Images (popv, /, annotate, src/annotate/popv/config.vsh.yaml, src/annotat...	12m 5s
build / Build and Deploy Docker Images (random_forest_annotation, /, annotate, src/annotate/random_forest...	3m 56s
build / Build and Deploy Docker Images (scanvi, /, annotate, src/annotate/scanvi/config.vsh.yaml, src/ann...	10m 36s
build / Build and Deploy Docker Images (svm_annotation, /, annotate, src/annotate/svm_annotation/config.v...	1m 30s
build / Build and Deploy Docker Images (leiden, /, cluster, src/cluster/leiden/config.vsh.yaml, src/clust...	2m 53s
build / Build and Deploy Docker Images (compress_h5mu, /, compression, src/compression/compress_h5mu/conf...	1m 15s
build / Build and Deploy Docker Images (tar_extract, /, compression, src/compression/tar_extract/config.v...	1m 3s
build / Build and Deploy Docker Images (from_10xh5_to_h5mu, /, convert, src/convert/from_10xh5_to_h5mu/co...	2m 30s
build / Build and Deploy Docker Images (from_10xmtx_to_h5mu, /, convert, src/convert/from_10xmtx_to_h5mu/...	2m 38s
build / Build and Deploy Docker Images (from_bd_to_10x_molecular_barcode_tags, /, convert, src/convert/fr...	55s
build / Build and Deploy Docker Images (from_bdrhap_to_h5mu, /, convert, src/convert/from_bdrhap_to_h5mu/...	1m 23s
build / Build and Deploy Docker Images (from_cellranger_multi_to_h5mu, /, convert, src/convert/from_cellr...	2m 9s
build / Build and Deploy Docker Images (from_h5ad_to_h5mu, /, convert, src/convert/from_h5ad_to_h5mu/conf...	1m 14s
build / Build and Deploy Docker Images (from_h5mu_to_h5ad, /, convert, src/convert/from_h5mu_to_h5ad/conf...	1m 23s
build / Build and Deploy Docker Images (from_h5mu_to_seurat, /, convert, src/convert/from_h5mu_to_seurat/...	3m 42s
build / Build and Deploy Docker Images (cellbender_remove_background, /, correction, src/correction/cellb...	11m 42s
build / Build and Deploy Docker Images (cellbender_remove_background_v0_2, /, correction, src/correction/...	5m 23s
build / Build and Deploy Docker Images (concatenate_h5mu, /, dataflow, src/dataflow/concatenate_h5mu/conf...	1m 25s
build / Build and Deploy Docker Images (merge, /, dataflow, src/dataflow/merge/config.vsh.yml, src/datafl...	1m 46s
build / Build and Deploy Docker Images (split_h5mu, /, dataflow, src/dataflow/split_h5mu/config.vsh.yaml,...	2m 38s
build / Build and Deploy Docker Images (split_h5mu_train_test, /, dataflow, src/dataflow/split_h5mu_train...	5m 13s
build / Build and Deploy Docker Images (split_modalities, /, dataflow, src/dataflow/split_modalities/conf...	1m 27s
build / Build and Deploy Docker Images (bcl2fastq, /, demux, src/demux/bcl2fastq/config.vsh.yaml, src/dem...	54s
build / Build and Deploy Docker Images (bcl_convert, /, demux, src/demux/bcl_convert/config.vsh.yaml, src...	54s
build / Build and Deploy Docker Images (cellranger_atac_mkfastq, /, demux, src/demux/cellranger_atac_mkfa...	1m 17s
build / Build and Deploy Docker Images (cellranger_mkfastq, /, demux, src/demux/cellranger_mkfastq/config...	1m 27s
build / Build and Deploy Docker Images (densmap, /, dimred, src/dimred/densmap/config.vsh.yaml, src/dimre...	1m 51s
build / Build and Deploy Docker Images (lsi, /, dimred, src/dimred/lsi/config.vsh.yaml, src/dimred/lsi/)	2m 35s
build / Build and Deploy Docker Images (pca, /, dimred, src/dimred/pca/config.vsh.yaml, src/dimred/pca/)	2m 23s
build / Build and Deploy Docker Images (tsne, /, dimred, src/dimred/tsne/config.vsh.yaml, src/dimred/tsne/)	3m 26s
build / Build and Deploy Docker Images (umap, /, dimred, src/dimred/umap/config.vsh.yaml, src/dimred/umap/)	1m 50s
build / Build and Deploy Docker Images (download_file, /, download, src/download/download_file/config.vsh...	2m 31s
build / Build and Deploy Docker Images (sync_test_resources, /, download, src/download/sync_test_resource...	2m 12s
build / Build and Deploy Docker Images (highly_variable_features_scanpy, /, feature_annotation, src/featu...	3m 7s
build / Build and Deploy Docker Images (score_genes_cell_cycle_scanpy, /, feature_annotation, src/feature...	2m 1s
build / Build and Deploy Docker Images (score_genes_scanpy, /, feature_annotation, src/feature_annotation...	2m 7s
build / Build and Deploy Docker Images (make_params, /, files, src/files/make_params/config.vsh.yaml, src...	1m 26s
build / Build and Deploy Docker Images (delimit_fraction, /, filter, src/filter/delimit_fraction/config.v...	2m 54s
build / Build and Deploy Docker Images (do_filter, /, filter, src/filter/do_filter/config.vsh.yaml, src/f...	1m 35s
build / Build and Deploy Docker Images (filter_with_counts, /, filter, src/filter/filter_with_counts/conf...	2m 38s
build / Build and Deploy Docker Images (filter_with_scrublet, /, filter, src/filter/filter_with_scrublet/...	2m 27s
build / Build and Deploy Docker Images (intersect_obs, /, filter, src/filter/intersect_obs/config.vsh.yam...	1m 42s
build / Build and Deploy Docker Images (remove_modality, /, filter, src/filter/remove_modality/config.vsh...	1m 19s
build / Build and Deploy Docker Images (subset_h5mu, /, filter, src/filter/subset_h5mu/config.vsh.yaml, s...	1m 25s
build / Build and Deploy Docker Images (subset_obsp, /, filter, src/filter/subset_obsp/config.vsh.yaml, s...	1m 54s
build / Build and Deploy Docker Images (bcftools, /, genetic_demux, src/genetic_demux/bcftools/config.vsh...	3m 2s
build / Build and Deploy Docker Images (cellsnp, /, genetic_demux, src/genetic_demux/cellsnp/config.vsh.y...	2m 42s
build / Build and Deploy Docker Images (demuxlet, /, genetic_demux, src/genetic_demux/demuxlet/config.vsh...	8m 46s
build / Build and Deploy Docker Images (dsc_pileup, /, genetic_demux, src/genetic_demux/dsc_pileup/config...	5m 7s
build / Build and Deploy Docker Images (freebayes, /, genetic_demux, src/genetic_demux/freebayes/config.v...	3m 36s
build / Build and Deploy Docker Images (freemuxlet, /, genetic_demux, src/genetic_demux/freemuxlet/config...	7m 43s
build / Build and Deploy Docker Images (samtools, /, genetic_demux, src/genetic_demux/samtools/config.vsh...	2m 33s
build / Build and Deploy Docker Images (scsplit, /, genetic_demux, src/genetic_demux/scsplit/config.vsh.y...	1m 52s
build / Build and Deploy Docker Images (souporcell, /, genetic_demux, src/genetic_demux/souporcell/config...	3m 42s
build / Build and Deploy Docker Images (vireo, /, genetic_demux, src/genetic_demux/vireo/config.vsh.yaml,...	1m 27s
build / Build and Deploy Docker Images (harmonypy, /, integrate, src/integrate/harmonypy/config.vsh.yaml,...	2m 25s
build / Build and Deploy Docker Images (scanorama, /, integrate, src/integrate/scanorama/config.vsh.yaml,...	3m 18s
build / Build and Deploy Docker Images (scarches, /, integrate, src/integrate/scarches/config.vsh.yaml, s...	13m 15s
build / Build and Deploy Docker Images (scvi, /, integrate, src/integrate/scvi/config.vsh.yaml, src/integ...	15m 58s
build / Build and Deploy Docker Images (totalvi, /, integrate, src/integrate/totalvi/config.vsh.yaml, src...	12m 41s
build / Build and Deploy Docker Images (lianapy, /, interpret, src/interpret/lianapy/config.vsh.yaml, src...	2m 5s
build / Build and Deploy Docker Images (knn, /, labels_transfer, src/labels_transfer/knn/config.vsh.yaml,...	1m 40s
build / Build and Deploy Docker Images (xgboost, /, labels_transfer, src/labels_transfer/xgboost/config.v...	2m 32s
build / Build and Deploy Docker Images (bd_rhapsody, /, mapping, src/mapping/bd_rhapsody/config.vsh.yaml,...	1m 55s
build / Build and Deploy Docker Images (cellranger_atac_count, /, mapping, src/mapping/cellranger_atac_co...	2m 38s
build / Build and Deploy Docker Images (cellranger_count, /, mapping, src/mapping/cellranger_count/config...	1m 31s
build / Build and Deploy Docker Images (cellranger_count_split, /, mapping, src/mapping/cellranger_count_...	59s
build / Build and Deploy Docker Images (cellranger_multi, /, mapping, src/mapping/cellranger_multi/config...	1m 42s
build / Build and Deploy Docker Images (htseq_count, /, mapping, src/mapping/htseq_count/config.vsh.yaml,...	1m 22s
build / Build and Deploy Docker Images (htseq_count_to_h5mu, /, mapping, src/mapping/htseq_count_to_h5mu/...	1m 33s
build / Build and Deploy Docker Images (multi_star, /, mapping, src/mapping/multi_star/config.vsh.yaml, s...	4m 49s
build / Build and Deploy Docker Images (multi_star_to_h5mu, /, mapping, src/mapping/multi_star_to_h5mu/co...	1m 13s
build / Build and Deploy Docker Images (samtools_sort, /, mapping, src/mapping/samtools_sort/config.vsh.y...	56s
build / Build and Deploy Docker Images (star_align, /, mapping, src/mapping/star_align/config.vsh.yaml, s...	4m 22s
build / Build and Deploy Docker Images (star_align_v273a, /, mapping, src/mapping/star_align_v273a/config...	3m 1s
build / Build and Deploy Docker Images (add_id, /, metadata, src/metadata/add_id/config.vsh.yaml, src/met...	1m 21s
build / Build and Deploy Docker Images (copy_obs, /, metadata, src/metadata/copy_obs/config.vsh.yaml, src...	2m 31s
build / Build and Deploy Docker Images (duplicate_var, /, metadata, src/metadata/duplicate_var/config.vsh...	4m 3s
build / Build and Deploy Docker Images (grep_annotation_column, /, metadata, src/metadata/grep_annotation...	1m 16s
build / Build and Deploy Docker Images (join_csv, /, metadata, src/metadata/join_csv/config.vsh.yml, src/...	1m 21s
build / Build and Deploy Docker Images (join_uns_to_obs, /, metadata, src/metadata/join_uns_to_obs/config...	1m 15s
build / Build and Deploy Docker Images (move_obsm_to_obs, /, metadata, src/metadata/move_obsm_to_obs/conf...	1m 15s
build / Build and Deploy Docker Images (bbknn, /, neighbors, src/neighbors/bbknn/config.vsh.yaml, src/nei...	2m 8s
build / Build and Deploy Docker Images (find_neighbors, /, neighbors, src/neighbors/find_neighbors/config...	2m 22s
build / Build and Deploy Docker Images (filter_10xh5, /, process_10xh5, src/process_10xh5/filter_10xh5/co...	4m 4s
build / Build and Deploy Docker Images (calculate_qc_metrics, /, qc, src/qc/calculate_qc_metrics/config.v...	3m 23s
build / Build and Deploy Docker Images (fastqc, /, qc, src/qc/fastqc/config.vsh.yaml, src/qc/fastqc/)	2m 1s
build / Build and Deploy Docker Images (multiqc, /, qc, src/qc/multiqc/config.vsh.yaml, src/qc/multiqc/)	2m 10s
build / Build and Deploy Docker Images (cellxgene_census, /, query, src/query/cellxgene_census/config.vsh...	2m 27s
build / Build and Deploy Docker Images (build_bdrhap_reference, /, reference, src/reference/build_bdrhap_...	1m 53s
build / Build and Deploy Docker Images (build_cellranger_arc_reference, /, reference, src/reference/build...	1m 23s
build / Build and Deploy Docker Images (build_cellranger_reference, /, reference, src/reference/build_cel...	1m 31s
build / Build and Deploy Docker Images (build_star_reference, /, reference, src/reference/build_star_refe...	3m 53s
build / Build and Deploy Docker Images (cellranger_mkgtf, /, reference, src/reference/cellranger_mkgtf/co...	1m 25s
build / Build and Deploy Docker Images (make_reference, /, reference, src/reference/make_reference/config...	53s
build / Build and Deploy Docker Images (mermaid, /, report, src/report/mermaid/config.vsh.yaml, src/repor...	2m 56s
build / Build and Deploy Docker Images (binning, /, scgpt, src/scgpt/binning/config.vsh.yaml, src/scgpt/b...	1m 11s
build / Build and Deploy Docker Images (cell_type_annotation, /, scgpt, src/scgpt/cell_type_annotation/co...	7m 12s
build / Build and Deploy Docker Images (cross_check_genes, /, scgpt, src/scgpt/cross_check_genes/config.v...	6m 31s
build / Build and Deploy Docker Images (embedding, /, scgpt, src/scgpt/embedding/config.vsh.yaml, src/scg...	6m 48s
build / Build and Deploy Docker Images (pad_tokenize, /, scgpt, src/scgpt/pad_tokenize/config.vsh.yaml, s...	6m 19s
build / Build and Deploy Docker Images (publish, /, transfer, src/transfer/publish/config.vsh.yaml, src/t...	2m 31s
build / Build and Deploy Docker Images (bpcells_regress_out, /, transform, src/transform/bpcells_regress_...	9m 28s
build / Build and Deploy Docker Images (clr, /, transform, src/transform/clr/config.vsh.yaml, src/transfo...	2m 20s
build / Build and Deploy Docker Images (delete_layer, /, transform, src/transform/delete_layer/config.vsh...	1m 20s
build / Build and Deploy Docker Images (log1p, /, transform, src/transform/log1p/config.vsh.yaml, src/tra...	1m 55s
build / Build and Deploy Docker Images (move_layer, /, transform, src/transform/move_layer/config.vsh.yam...	2m 36s
build / Build and Deploy Docker Images (normalize_total, /, transform, src/transform/normalize_total/conf...	2m 50s
build / Build and Deploy Docker Images (regress_out, /, transform, src/transform/regress_out/config.vsh.y...	2m 16s
build / Build and Deploy Docker Images (scale, /, transform, src/transform/scale/config.vsh.yaml, src/tra...	1m 51s
build / Build and Deploy Docker Images (tfidf, /, transform, src/transform/tfidf/config.vsh.yaml, src/tra...	4m 26s
build / Build and Deploy Docker Images (scvelo, /, velocity, src/velocity/scvelo/config.vsh.yaml, src/vel...	8m 54s
build / Build and Deploy Docker Images (velocyto, /, velocity, src/velocity/velocyto/config.vsh.yaml, src...	2m 47s
build / Build and Deploy Docker Images (velocyto_to_h5mu, /, convert, src/velocity/velocyto_to_h5mu/confi...	2m 40s
build / Build and Deploy Docker Images (bd_rhapsody_test, /, test_workflows/ingestion, src/workflows/test...	3m 9s
build / Build and Deploy Docker Images (cellranger_mapping_test, /, test_workflows/ingestion, src/workflo...	1m 34s
build / Build and Deploy Docker Images (cellranger_multi_test, /, test_workflows/ingestion, src/workflows...	3m 18s
build / Build and Deploy Docker Images (cellranger_postprocessing_test, /, test_workflows/ingestion, src/...	2m 58s
build / Build and Deploy Docker Images (conversion_test, /, test_workflows/ingestion, src/workflows/test_...	4m 5s
build / Build and Deploy Docker Images (dimensionality_reduction_test, /, test_workflows/multiomics, src/...	1m 18s
build / Build and Deploy Docker Images (workflow_test, /, test_workflows/multiomics/process_batches, src/...	1m 23s
build / Build and Deploy Docker Images (workflow_test2, /, test_workflows/multiomics/process_batches, src...	1m 24s
build / Build and Deploy Docker Images (split_modalities_test, /, test_workflows/multiomics, src/workflow...	1m 26s
build / Build and Deploy Docker Images (qc_test, /, test_workflows/qc, src/workflows/test_workflows/qc/co...	3m 45s
integration_test (gdo_singlesample, workflows/gdo, src/workflows/gdo/gdo_singlesample//test.nf, t...	10m 11s
integration_test (bd_rhapsody, workflows/ingestion, src/workflows/ingestion/bd_rhapsody//test.nf,...	18m 9s
integration_test (cellranger_mapping, workflows/ingestion, src/workflows/ingestion/cellranger_map...	1h 9m 22s
integration_test (cellranger_multi, workflows/ingestion, src/workflows/ingestion/cellranger_multi...	1h 7m 28s
integration_test (cellranger_multi, workflows/ingestion, src/workflows/ingestion/cellranger_multi...	1h 7m 48s
integration_test (cellranger_postprocessing, workflows/ingestion, src/workflows/ingestion/cellran...	13m 28s
integration_test (cellranger_postprocessing, workflows/ingestion, src/workflows/ingestion/cellran...	8m 16s
integration_test (conversion, workflows/ingestion, src/workflows/ingestion/conversion//test.nf, t...	9m 14s
integration_test (demux, workflows/ingestion, src/workflows/ingestion/demux//test.nf, test_wf, sr...	1h 7m 27s
integration_test (make_reference, workflows/ingestion, src/workflows/ingestion/make_reference//te...	1h 7m 22s
integration_test (bbknn_leiden, workflows/integration, src/workflows/integration/bbknn_leiden//te...	9m 15s
integration_test (bbknn_leiden, workflows/integration, src/workflows/integration/bbknn_leiden//te...	9m 12s
integration_test (harmony_leiden, workflows/integration, src/workflows/integration/harmony_leiden...	10m 53s
integration_test (harmony_leiden, workflows/integration, src/workflows/integration/harmony_leiden...	10m 7s
integration_test (scanorama_leiden, workflows/integration, src/workflows/integration/scanorama_le...	11m 53s
integration_test (scanorama_leiden, workflows/integration, src/workflows/integration/scanorama_le...	12m 5s
integration_test (scgpt_leiden, workflows/integration, src/workflows/integration/scgpt_leiden//te...	29m 3s
integration_test (scgpt_leiden, workflows/integration, src/workflows/integration/scgpt_leiden//te...	21m 29s
integration_test (scvi_leiden, workflows/integration, src/workflows/integration/scvi_leiden//test...	15m 49s
integration_test (totalvi_leiden, workflows/integration, src/workflows/integration/totalvi_leiden...	18m 31s
integration_test (dimensionality_reduction, workflows/multiomics, src/workflows/multiomics/dimens...	12m 51s
integration_test (process_batches, workflows/multiomics, src/workflows/multiomics/process_batches...	17m 33s
integration_test (process_batches, workflows/multiomics, src/workflows/multiomics/process_batches...	14m 19s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	15m 50s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	15m 18s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	14m 21s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	14m 6s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	14m 45s
integration_test (split_modalities, workflows/multiomics, src/workflows/multiomics/split_modaliti...	7m 42s
integration_test (prot_multisample, workflows/prot, src/workflows/prot/prot_multisample//test.nf,...	8m 48s
integration_test (prot_singlesample, workflows/prot, src/workflows/prot/prot_singlesample//test.n...	7m 52s
integration_test (qc, workflows/qc, src/workflows/qc/qc//test.nf, test_wf, src/workflows/qc/qc/co...	8m 52s
integration_test (rna_multisample, workflows/rna, src/workflows/rna/rna_multisample//test.nf, tes...	9m 21s
integration_test (rna_singlesample, workflows/rna, src/workflows/rna/rna_singlesample//test.nf, t...	8m 44s
integration_test (rna_singlesample, workflows/rna, src/workflows/rna/rna_singlesample//test.nf, t...	10m 37s
	18h 59m 22s

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integration test #644

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integration test #644

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