integration test #717

Run time

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Job	Run time
sync_s3	2m 38s
build / Build and push target folder	5m 40s
build / celltypist - annotate - Build and push docker image	2m 28s
build / onclass - annotate - Build and push docker image	12m 5s
build / popv - annotate - Build and push docker image	15m 56s
build / random_forest_annotation - annotate - Build and push docker image	1m 48s
build / scanvi - annotate - Build and push docker image	10m 17s
build / svm_annotation - annotate - Build and push docker image	2m 44s
build / leiden - cluster - Build and push docker image	2m 53s
build / compress_h5mu - compression - Build and push docker image	1m 10s
build / tar_extract - compression - Build and push docker image	36s
build / from_10xh5_to_h5mu - convert - Build and push docker image	2m 24s
build / from_10xmtx_to_h5mu - convert - Build and push docker image	1m 54s
build / from_bd_to_10x_molecular_barcode_tags - convert - Build and push docker image	54s
build / from_bdrhap_to_h5mu - convert - Build and push docker image	1m 39s
build / from_cellranger_multi_to_h5mu - convert - Build and push docker image	2m 38s
build / from_h5ad_to_h5mu - convert - Build and push docker image	2m 1s
build / from_h5mu_to_h5ad - convert - Build and push docker image	1m 27s
build / from_h5mu_to_seurat - convert - Build and push docker image	2m 35s
build / cellbender_remove_background - correction - Build and push docker image	9m 20s
build / cellbender_remove_background_v0_2 - correction - Build and push docker image	5m 21s
build / concatenate_h5mu - dataflow - Build and push docker image	1m 40s
build / merge - dataflow - Build and push docker image	1m 13s
build / split_h5mu - dataflow - Build and push docker image	1m 15s
build / split_h5mu_train_test - dataflow - Build and push docker image	2m 23s
build / split_modalities - dataflow - Build and push docker image	2m 6s
build / bcl2fastq - demux - Build and push docker image	49s
build / bcl_convert - demux - Build and push docker image	51s
build / cellranger_atac_mkfastq - demux - Build and push docker image	2m 8s
build / cellranger_mkfastq - demux - Build and push docker image	1m 26s
build / densmap - dimred - Build and push docker image	2m 30s
build / lsi - dimred - Build and push docker image	2m 2s
build / pca - dimred - Build and push docker image	2m 27s
build / tsne - dimred - Build and push docker image	2m 14s
build / umap - dimred - Build and push docker image	3m 6s
build / download_file - download - Build and push docker image	1m 22s
build / sync_test_resources - download - Build and push docker image	54s
build / highly_variable_features_scanpy - feature_annotation - Build and push docker image	2m 1s
build / score_genes_cell_cycle_scanpy - feature_annotation - Build and push docker image	2m 29s
build / score_genes_scanpy - feature_annotation - Build and push docker image	2m 36s
build / make_params - files - Build and push docker image	1m 19s
build / delimit_fraction - filter - Build and push docker image	1m 10s
build / do_filter - filter - Build and push docker image	2m 30s
build / filter_with_counts - filter - Build and push docker image	1m 12s
build / filter_with_scrublet - filter - Build and push docker image	2m 17s
build / intersect_obs - filter - Build and push docker image	1m 15s
build / remove_modality - filter - Build and push docker image	1m 10s
build / subset_h5mu - filter - Build and push docker image	1m 16s
build / subset_obsp - filter - Build and push docker image	2m 1s
build / bcftools - genetic_demux - Build and push docker image	2m 18s
build / cellsnp - genetic_demux - Build and push docker image	2m 22s
build / demuxlet - genetic_demux - Build and push docker image	7m 28s
build / dsc_pileup - genetic_demux - Build and push docker image	4m 53s
build / freebayes - genetic_demux - Build and push docker image	1m 2s
build / freemuxlet - genetic_demux - Build and push docker image	6m 57s
build / samtools - genetic_demux - Build and push docker image	3m 52s
build / scsplit - genetic_demux - Build and push docker image	3m 52s
build / souporcell - genetic_demux - Build and push docker image	2m 7s
build / vireo - genetic_demux - Build and push docker image	2m 7s
build / harmonypy - integrate - Build and push docker image	3m 10s
build / scanorama - integrate - Build and push docker image	2m 21s
build / scarches - integrate - Build and push docker image	16m 4s
build / scvi - integrate - Build and push docker image	19m 5s
build / totalvi - integrate - Build and push docker image	16m 37s
build / lianapy - interpret - Build and push docker image	1m 51s
build / knn - labels_transfer - Build and push docker image	1m 42s
build / xgboost - labels_transfer - Build and push docker image	2m 42s
build / bd_rhapsody - mapping - Build and push docker image	1m 39s
build / cellranger_atac_count - mapping - Build and push docker image	1m 13s
build / cellranger_count - mapping - Build and push docker image	1m 26s
build / cellranger_count_split - mapping - Build and push docker image	2m 0s
build / cellranger_multi - mapping - Build and push docker image	1m 33s
build / htseq_count - mapping - Build and push docker image	1m 15s
build / htseq_count_to_h5mu - mapping - Build and push docker image	1m 16s
build / multi_star - mapping - Build and push docker image	4m 33s
build / multi_star_to_h5mu - mapping - Build and push docker image	1m 40s
build / samtools_sort - mapping - Build and push docker image	1m 42s
build / star_align - mapping - Build and push docker image	3m 41s
build / star_align_v273a - mapping - Build and push docker image	2m 43s
build / add_id - metadata - Build and push docker image	1m 45s
build / duplicate_obs - metadata - Build and push docker image	1m 43s
build / duplicate_var - metadata - Build and push docker image	1m 56s
build / grep_annotation_column - metadata - Build and push docker image	2m 52s
build / join_csv - metadata - Build and push docker image	2m 23s
build / join_uns_to_obs - metadata - Build and push docker image	1m 31s
build / move_obsm_to_obs - metadata - Build and push docker image	1m 17s
build / bbknn - neighbors - Build and push docker image	2m 7s
build / find_neighbors - neighbors - Build and push docker image	3m 11s
build / filter_10xh5 - process_10xh5 - Build and push docker image	2m 32s
build / calculate_atac_qc_metrics - qc - Build and push docker image	2m 35s
build / calculate_qc_metrics - qc - Build and push docker image	1m 11s
build / fastqc - qc - Build and push docker image	1m 37s
build / multiqc - qc - Build and push docker image	1m 44s
build / cellxgene_census - query - Build and push docker image	2m 6s
build / build_bdrhap_reference - reference - Build and push docker image	1m 37s
build / build_cellranger_arc_reference - reference - Build and push docker image	2m 25s
build / build_cellranger_reference - reference - Build and push docker image	2m 24s
build / build_star_reference - reference - Build and push docker image	4m 15s
build / cellranger_mkgtf - reference - Build and push docker image	1m 19s
build / make_reference - reference - Build and push docker image	1m 1s
build / mermaid - report - Build and push docker image	3m 54s
build / binning - scgpt - Build and push docker image	1m 34s
build / cell_type_annotation - scgpt - Build and push docker image	7m 7s
build / cross_check_genes - scgpt - Build and push docker image	6m 43s
build / embedding - scgpt - Build and push docker image	6m 52s
build / pad_tokenize - scgpt - Build and push docker image	7m 9s
build / publish - transfer - Build and push docker image	1m 42s
build / bpcells_regress_out - transform - Build and push docker image	9m 1s
build / clr - transform - Build and push docker image	2m 11s
build / delete_layer - transform - Build and push docker image	1m 16s
build / log1p - transform - Build and push docker image	1m 46s
build / move_layer - transform - Build and push docker image	1m 10s
build / normalize_total - transform - Build and push docker image	3m 20s
build / regress_out - transform - Build and push docker image	2m 7s
build / scale - transform - Build and push docker image	1m 46s
build / tfidf - transform - Build and push docker image	2m 7s
build / scvelo - velocity - Build and push docker image	2m 59s
build / velocyto - velocity - Build and push docker image	2m 8s
build / velocyto_to_h5mu - convert - Build and push docker image	2m 24s
integration_test (scgpt_annotation, workflows/annotation, src/workflows/annotation/scgpt_annotati...	15m 37s
integration_test (scgpt_integration_knn, workflows/annotation, src/workflows/annotation/scgpt_int...	18m 29s
integration_test (gdo_singlesample, workflows/gdo, src/workflows/gdo/gdo_singlesample//test.nf, t...	4m 2s
integration_test (bd_rhapsody, workflows/ingestion, src/workflows/ingestion/bd_rhapsody//test.nf,...	16m 44s
integration_test (cellranger_mapping, workflows/ingestion, src/workflows/ingestion/cellranger_map...	7m 41s
integration_test (cellranger_multi, workflows/ingestion, src/workflows/ingestion/cellranger_multi...	9m 34s
integration_test (cellranger_multi, workflows/ingestion, src/workflows/ingestion/cellranger_multi...	8m 7s
integration_test (cellranger_postprocessing, workflows/ingestion, src/workflows/ingestion/cellran...	11m 38s
integration_test (cellranger_postprocessing, workflows/ingestion, src/workflows/ingestion/cellran...	7m 21s
integration_test (conversion, workflows/ingestion, src/workflows/ingestion/conversion//test.nf, t...	7m 4s
integration_test (demux, workflows/ingestion, src/workflows/ingestion/demux//test.nf, test_wf, sr...	7m 55s
integration_test (make_reference, workflows/ingestion, src/workflows/ingestion/make_reference//te...	20m 43s
integration_test (bbknn_leiden, workflows/integration, src/workflows/integration/bbknn_leiden//te...	5m 35s
integration_test (bbknn_leiden, workflows/integration, src/workflows/integration/bbknn_leiden//te...	6m 36s
integration_test (harmony_leiden, workflows/integration, src/workflows/integration/harmony_leiden...	7m 15s
integration_test (harmony_leiden, workflows/integration, src/workflows/integration/harmony_leiden...	5m 51s
integration_test (scanorama_leiden, workflows/integration, src/workflows/integration/scanorama_le...	6m 30s
integration_test (scanorama_leiden, workflows/integration, src/workflows/integration/scanorama_le...	6m 6s
integration_test (scgpt_leiden, workflows/integration, src/workflows/integration/scgpt_leiden//te...	25m 15s
integration_test (scgpt_leiden, workflows/integration, src/workflows/integration/scgpt_leiden//te...	17m 16s
integration_test (scvi_leiden, workflows/integration, src/workflows/integration/scvi_leiden//test...	10m 21s
integration_test (totalvi_leiden, workflows/integration, src/workflows/integration/totalvi_leiden...	13m 0s
integration_test (dimensionality_reduction, workflows/multiomics, src/workflows/multiomics/dimens...	7m 44s
integration_test (process_batches, workflows/multiomics, src/workflows/multiomics/process_batches...	12m 41s
integration_test (process_batches, workflows/multiomics, src/workflows/multiomics/process_batches...	13m 23s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	11m 49s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	11m 29s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	11m 4s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	10m 4s
integration_test (process_samples, workflows/multiomics, src/workflows/multiomics/process_samples...	10m 16s
integration_test (split_modalities, workflows/multiomics, src/workflows/multiomics/split_modaliti...	4m 38s
integration_test (prot_multisample, workflows/prot, src/workflows/prot/prot_multisample//test.nf,...	4m 45s
integration_test (prot_singlesample, workflows/prot, src/workflows/prot/prot_singlesample//test.n...	4m 39s
integration_test (qc, workflows/qc, src/workflows/qc/qc//test.nf, test_wf, src/workflows/qc/qc/co...	5m 1s
integration_test (rna_multisample, workflows/rna, src/workflows/rna/rna_multisample//test.nf, tes...	6m 31s
integration_test (rna_singlesample, workflows/rna, src/workflows/rna/rna_singlesample//test.nf, t...	4m 54s
integration_test (rna_singlesample, workflows/rna, src/workflows/rna/rna_singlesample//test.nf, t...	5m 40s
	12h 17m 26s

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integration test #717

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integration test #717

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