integration test #1309

Run time

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Job	Run time
build / Build and push target folder	4m 24s
sync_s3	4m 49s
build / celltypist - annotate - Build and push docker image	6m 41s
build / onclass - annotate - Build and push docker image	8m 44s
build / scanvi - annotate - Build and push docker image	6m 54s
build / consensus_vote - annotate - Build and push docker image	1m 38s
build / popv - annotate - Build and push docker image	6m 13s
build / cellranger_atac_mkfastq - demux - Build and push docker image	3m 1s
build / from_cellranger_multi_to_h5mu - convert - Build and push docker image	3m 23s
build / score_genes_scanpy - feature_annotation - Build and push docker image	3m 2s
build / from_h5mu_or_h5ad_to_seurat - convert - Build and push docker image	4m 58s
build / from_bd_to_10x_molecular_barcode_tags - convert - Build and push docker image	1m 13s
build / intersect_obs - filter - Build and push docker image	2m 36s
build / from_seurat_to_h5mu - convert - Build and push docker image	4m 31s
build / random_forest_annotation - annotate - Build and push docker image	1m 35s
build / dsc_pileup - genetic_demux - Build and push docker image	8m 4s
build / samtools - genetic_demux - Build and push docker image	2m 10s
build / singler - annotate - Build and push docker image	3m 12s
build / lsi - dimred - Build and push docker image	5m 19s
build / score_genes_cell_cycle_scanpy - feature_annotation - Build and push docker image	2m 15s
build / from_10xh5_to_h5mu - convert - Build and push docker image	4m 59s
build / remove_modality - filter - Build and push docker image	3m 2s
build / pca - dimred - Build and push docker image	3m 6s
build / compress_h5mu - compression - Build and push docker image	1m 44s
build / from_h5mu_to_h5ad - convert - Build and push docker image	1m 47s
build / filter_with_quantile - filter - Build and push docker image	4m 29s
build / create_pseudobulk - differential_expression - Build and push docker image	2m 12s
build / delimit_counts - filter - Build and push docker image	1m 35s
build / tsne - dimred - Build and push docker image	3m 39s
build / filter_with_scrublet - filter - Build and push docker image	4m 12s
build / merge - dataflow - Build and push docker image	2m 19s
build / bcl2fastq - demux - Build and push docker image	1m 42s
build / cellbender_remove_background - correction - Build and push docker image	8m 35s
build / cellsnp - genetic_demux - Build and push docker image	3m 58s
build / filter_with_counts - filter - Build and push docker image	3m 59s
build / from_h5mu_to_seurat - convert - Build and push docker image	3m 9s
build / highly_variable_features_scanpy - feature_annotation - Build and push docker image	3m 40s
build / densmap - dimred - Build and push docker image	2m 55s
build / download_file - download - Build and push docker image	58s
build / from_10xmtx_to_h5mu - convert - Build and push docker image	2m 54s
build / umap - dimred - Build and push docker image	4m 2s
build / deseq2 - differential_expression - Build and push docker image	4m 4s
build / leiden - cluster - Build and push docker image	2m 57s
build / from_h5ad_to_h5mu - convert - Build and push docker image	1m 50s
build / from_bdrhap_to_h5mu - convert - Build and push docker image	2m 38s
build / freebayes - genetic_demux - Build and push docker image	2m 31s
build / svm_annotation - annotate - Build and push docker image	3m 19s
build / do_filter - filter - Build and push docker image	2m 13s
build / tar_extract - compression - Build and push docker image	1m 3s
build / delimit_fraction - filter - Build and push docker image	2m 41s
build / bcftools - genetic_demux - Build and push docker image	4m 9s
build / split_modalities - dataflow - Build and push docker image	2m 6s
build / filter_with_pattern - filter - Build and push docker image	2m 27s
build / from_h5mu_or_h5ad_to_tiledb - convert - Build and push docker image	2m 12s
build / cellranger_mkfastq - demux - Build and push docker image	5m 15s
build / from_h5ad_to_seurat - convert - Build and push docker image	4m 3s
build / subset_h5mu - filter - Build and push docker image	4m 34s
build / bcl_convert - demux - Build and push docker image	1m 11s
build / freemuxlet - genetic_demux - Build and push docker image	8m 21s
build / align_query_reference - feature_annotation - Build and push docker image	4m 38s
build / concatenate_h5mu - dataflow - Build and push docker image	3m 34s
build / from_tiledb_to_h5mu - convert - Build and push docker image	2m 28s
build / demuxlet - genetic_demux - Build and push docker image	11m 6s
build / split_h5mu - dataflow - Build and push docker image	1m 45s
build / subset_obsp - filter - Build and push docker image	3m 21s
build / make_params - files - Build and push docker image	1m 44s
build / scanorama - integrate - Build and push docker image	4m 51s
build / harmonypy - integrate - Build and push docker image	4m 23s
build / vireo - genetic_demux - Build and push docker image	2m 53s
build / cellranger_count_split - mapping - Build and push docker image	3m 58s
build / souporcell - genetic_demux - Build and push docker image	3m 8s
build / totalvi_scarches - integrate - Build and push docker image	5m 16s
build / totalvi - integrate - Build and push docker image	9m 49s
build / lianapy - interpret - Build and push docker image	1m 59s
build / scarches - integrate - Build and push docker image	5m 3s
build / scvi - integrate - Build and push docker image	3m 59s
build / xgboost - labels_transfer - Build and push docker image	2m 53s
build / cellranger_atac_count - mapping - Build and push docker image	4m 5s
build / add_id - metadata - Build and push docker image	2m 28s
build / knn - labels_transfer - Build and push docker image	1m 58s
build / htseq_count_to_h5mu - mapping - Build and push docker image	3m 47s
build / join_uns_to_obs - metadata - Build and push docker image	1m 31s
build / cellmapper - labels_transfer - Build and push docker image	3m 53s
build / multi_star - mapping - Build and push docker image	6m 49s
build / join_csv - metadata - Build and push docker image	3m 24s
build / htseq_count - mapping - Build and push docker image	3m 53s
build / star_align_v273a - mapping - Build and push docker image	3m 2s
build / cellranger_multi - mapping - Build and push docker image	2m 31s
build / multiqc - qc - Build and push docker image	3m 19s
build / star_align - mapping - Build and push docker image	4m 35s
build / samtools_sort - mapping - Build and push docker image	2m 0s
build / filter_10xh5 - process_10xh5 - Build and push docker image	3m 18s
build / cellranger_count - mapping - Build and push docker image	2m 14s
build / grep_annotation_column - metadata - Build and push docker image	2m 37s
build / bd_rhapsody - mapping - Build and push docker image	2m 50s
build / scsplit - genetic_demux - Build and push docker image	4m 18s
build / calculate_atac_qc_metrics - qc - Build and push docker image	2m 41s
build / multi_star_to_h5mu - mapping - Build and push docker image	2m 26s
build / move_obsm_to_obs - metadata - Build and push docker image	3m 50s
build / fastqc - qc - Build and push docker image	3m 2s
build / tiledb_healthcheck - query - Build and push docker image	8m 9s
build / make_reference - reference - Build and push docker image	1m 53s
build / bbknn - neighbors - Build and push docker image	3m 28s
build / build_cellranger_reference - reference - Build and push docker image	4m 8s
build / bpcells_regress_out - transform - Build and push docker image	11m 17s
build / build_bdrhap_reference - reference - Build and push docker image	2m 0s
build / cellxgene_census - query - Build and push docker image	4m 31s
build / calculate_qc_metrics - qc - Build and push docker image	1m 50s
build / move_mudata_obs_to_tiledb - tiledb - Build and push docker image	3m 16s
build / find_neighbors - neighbors - Build and push docker image	2m 59s
build / regress_out - transform - Build and push docker image	4m 3s
build / mermaid - report - Build and push docker image	3m 45s
build / build_star_reference - reference - Build and push docker image	4m 38s
build / normalize_total - transform - Build and push docker image	2m 3s
build / build_cellranger_arc_reference - reference - Build and push docker image	2m 14s
build / delete_layer - transform - Build and push docker image	1m 40s
build / velocyto - velocity - Build and push docker image	6m 32s
build / move_layer - transform - Build and push docker image	2m 19s
build / scvelo - velocity - Build and push docker image	4m 32s
build / clr - transform - Build and push docker image	2m 28s
build / clear_slots - transform - Build and push docker image	2m 40s
build / move_mudata_obsm_to_tiledb - tiledb - Build and push docker image	3m 7s
build / tfidf - transform - Build and push docker image	3m 13s
build / move_mudata_obsp_to_tiledb - tiledb - Build and push docker image	6m 44s
build / log1p - transform - Build and push docker image	3m 16s
build / velocyto_to_h5mu - convert - Build and push docker image	3m 14s
build / scale - transform - Build and push docker image	3m 36s
build / cellranger_mkgtf - reference - Build and push docker image	3m 40s
integration_test (celltypist, workflows/annotation, src/workflows/annotation/celltypist//test.nf,...	10m 42s
integration_test (scvi_knn, workflows/annotation, src/workflows/annotation/scvi_knn//test.nf, tes...	17m 11s
integration_test (scanvi_scarches, workflows/annotation, src/workflows/annotation/scanvi_scarches...	10m 45s
integration_test (gdo_singlesample, workflows/gdo, src/workflows/gdo/gdo_singlesample//test.nf, t...	5m 3s
integration_test (pseudobulk_deseq2, workflows/differential_expression, src/workflows/differentia...	7m 28s
integration_test (demux, workflows/ingestion, src/workflows/ingestion/demux//test.nf, test_wf, sr...	7m 4s
integration_test (harmony_knn, workflows/annotation, src/workflows/annotation/harmony_knn//test.n...	14m 15s
integration_test (scvi_leiden, workflows/integration, src/workflows/integration/scvi_leiden//test...	13m 57s
integration_test (process_singlesample, workflows/multiomics, src/workflows/multiomics/process_si...	10m 2s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	16m 33s
integration_test (bd_rhapsody, workflows/ingestion, src/workflows/ingestion/bd_rhapsody//test.nf,...	16m 20s
integration_test (harmony_leiden, workflows/integration, src/workflows/integration/harmony_leiden...	12m 11s
integration_test (cellranger_multi, workflows/ingestion, src/workflows/ingestion/cellranger_multi...	10m 36s
integration_test (make_reference, workflows/ingestion, src/workflows/ingestion/make_reference//te...	17m 54s
integration_test (log_normalize, workflows/rna, src/workflows/rna/log_normalize//test.nf, test_wf...	4m 56s
integration_test (rna_multisample, workflows/rna, src/workflows/rna/rna_multisample//test.nf, tes...	7m 44s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	17m 10s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	18m 19s
integration_test (totalvi_leiden, workflows/integration, src/workflows/integration/totalvi_leiden...	11m 7s
integration_test (process_batches, workflows/multiomics, src/workflows/multiomics/process_batches...	14m 52s
integration_test (cellranger_postprocessing, workflows/ingestion, src/workflows/ingestion/cellran...	7m 54s
integration_test (rna_singlesample, workflows/rna, src/workflows/rna/rna_singlesample//test.nf, t...	6m 3s
integration_test (dimensionality_reduction, workflows/multiomics, src/workflows/multiomics/dimens...	7m 34s
integration_test (conversion, workflows/ingestion, src/workflows/ingestion/conversion//test.nf, t...	9m 4s
integration_test (process_batches, workflows/multiomics, src/workflows/multiomics/process_batches...	17m 7s
integration_test (cellranger_multi, workflows/ingestion, src/workflows/ingestion/cellranger_multi...	12m 7s
integration_test (split_h5mu, workflows/multiomics, src/workflows/multiomics/split_h5mu//test.nf,...	5m 40s
integration_test (process_singlesample, workflows/multiomics, src/workflows/multiomics/process_si...	9m 43s
integration_test (prot_singlesample, workflows/prot, src/workflows/prot/prot_singlesample//test.n...	6m 35s
integration_test (cellranger_mapping, workflows/ingestion, src/workflows/ingestion/cellranger_map...	9m 38s
integration_test (scvi_leiden, workflows/integration, src/workflows/integration/scvi_leiden//test...	11m 26s
integration_test (process_singlesample, workflows/multiomics, src/workflows/multiomics/process_si...	10m 24s
integration_test (bbknn_leiden, workflows/integration, src/workflows/integration/bbknn_leiden//te...	6m 40s
integration_test (bbknn_leiden, workflows/integration, src/workflows/integration/bbknn_leiden//te...	7m 17s
integration_test (rna_singlesample, workflows/rna, src/workflows/rna/rna_singlesample//test.nf, t...	7m 37s
integration_test (qc, workflows/qc, src/workflows/qc/qc//test.nf, test_wf, src/workflows/qc/qc/co...	5m 58s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	16m 59s
integration_test (split_modalities, workflows/multiomics, src/workflows/multiomics/split_modaliti...	5m 22s
integration_test (prot_multisample, workflows/prot, src/workflows/prot/prot_multisample//test.nf,...	6m 21s
integration_test (cellranger_postprocessing, workflows/ingestion, src/workflows/ingestion/cellran...	11m 13s
integration_test (harmony_leiden, workflows/integration, src/workflows/integration/harmony_leiden...	8m 42s
integration_test (scanorama_leiden, workflows/integration, src/workflows/integration/scanorama_le...	8m 14s
integration_test (process_batches, workflows/multiomics, src/workflows/multiomics/process_batches...	16m 13s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	15m 39s
integration_test (totalvi_scarches_leiden, workflows/integration, src/workflows/integration/total...	13m 31s
integration_test (harmony_leiden, workflows/integration, src/workflows/integration/harmony_leiden...	8m 20s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	18m 8s
integration_test (scanorama_leiden, workflows/integration, src/workflows/integration/scanorama_le...	7m 21s
	16h 30m 45s

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integration test #1309

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integration test #1309

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Run time