Build

Cell type annotation: scGPT workflow (#832) #1122

Triggered via push December 5, 2024 09:49

DriesSchaumont

pushed e11f4fd

main

Status Success

Total duration 1h 8m 0s

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main-build.yml

on: push

Build and push target folder

5m 55s

Matrix: build_and_deploy_docker_containers

Annotations

117 warnings

Build and push target folder

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bcl_convert - demux - Build and push docker image

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add_id - metadata - Build and push docker image

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bcftools - genetic_demux - Build and push docker image

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bcl2fastq - demux - Build and push docker image

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bbknn - neighbors - Build and push docker image

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build_bdrhap_reference - reference - Build and push docker image

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build_cellranger_arc_reference - reference - Build and push docker image

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binning - scgpt - Build and push docker image

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calculate_qc_metrics - qc - Build and push docker image

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bd_rhapsody - mapping - Build and push docker image

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cellranger_atac_mkfastq - demux - Build and push docker image

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build_cellranger_reference - reference - Build and push docker image

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cellranger_count - mapping - Build and push docker image

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cellranger_mkfastq - demux - Build and push docker image

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cellranger_atac_count - mapping - Build and push docker image

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cellranger_count_split - mapping - Build and push docker image

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concatenate_h5mu - dataflow - Build and push docker image

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build_star_reference - reference - Build and push docker image

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cellranger_mkgtf - reference - Build and push docker image

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compress_h5mu - compression - Build and push docker image

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download_file - download - Build and push docker image

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cellsnp - genetic_demux - Build and push docker image

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clr - transform - Build and push docker image

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cellranger_multi - mapping - Build and push docker image

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delete_layer - transform - Build and push docker image

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celltypist - annotate - Build and push docker image

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delimit_fraction - filter - Build and push docker image

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duplicate_obs - metadata - Build and push docker image

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cellbender_remove_background_v0_2 - correction - Build and push docker image

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cellxgene_census - query - Build and push docker image

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duplicate_var - metadata - Build and push docker image

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densmap - dimred - Build and push docker image

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do_filter - filter - Build and push docker image

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find_neighbors - neighbors - Build and push docker image

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filter_10xh5 - process_10xh5 - Build and push docker image

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freebayes - genetic_demux - Build and push docker image

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cell_type_annotation - scgpt - Build and push docker image

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from_10xmtx_to_h5mu - convert - Build and push docker image

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from_bd_to_10x_molecular_barcode_tags - convert - Build and push docker image

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dsc_pileup - genetic_demux - Build and push docker image

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fastqc - qc - Build and push docker image

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from_10xh5_to_h5mu - convert - Build and push docker image

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from_h5ad_to_h5mu - convert - Build and push docker image

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grep_annotation_column - metadata - Build and push docker image

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filter_with_scrublet - filter - Build and push docker image

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from_cellranger_multi_to_h5mu - convert - Build and push docker image

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cross_check_genes - scgpt - Build and push docker image

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demuxlet - genetic_demux - Build and push docker image

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filter_with_counts - filter - Build and push docker image

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from_h5mu_to_seurat - convert - Build and push docker image

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intersect_obs - filter - Build and push docker image

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bpcells_regress_out - transform - Build and push docker image

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htseq_count_to_h5mu - mapping - Build and push docker image

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join_csv - metadata - Build and push docker image

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from_bdrhap_to_h5mu - convert - Build and push docker image

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from_h5mu_to_h5ad - convert - Build and push docker image

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harmonypy - integrate - Build and push docker image

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move_layer - transform - Build and push docker image

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htseq_count - mapping - Build and push docker image

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move_obsm_to_obs - metadata - Build and push docker image

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lianapy - interpret - Build and push docker image

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highly_variable_features_scanpy - feature_annotation - Build and push docker image

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embedding - scgpt - Build and push docker image

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leiden - cluster - Build and push docker image

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log1p - transform - Build and push docker image

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multi_star_to_h5mu - mapping - Build and push docker image

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make_reference - reference - Build and push docker image

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make_params - files - Build and push docker image

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join_uns_to_obs - metadata - Build and push docker image

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knn - labels_transfer - Build and push docker image

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publish - transfer - Build and push docker image

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multiqc - qc - Build and push docker image

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cellbender_remove_background - correction - Build and push docker image

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merge - dataflow - Build and push docker image

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lsi - dimred - Build and push docker image

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random_forest_annotation - annotate - Build and push docker image

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remove_modality - filter - Build and push docker image

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freemuxlet - genetic_demux - Build and push docker image

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mermaid - report - Build and push docker image

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normalize_total - transform - Build and push docker image

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samtools_sort - mapping - Build and push docker image

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pca - dimred - Build and push docker image

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scale - transform - Build and push docker image

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scanorama - integrate - Build and push docker image

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regress_out - transform - Build and push docker image

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scsplit - genetic_demux - Build and push docker image

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score_genes_cell_cycle_scanpy - feature_annotation - Build and push docker image

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score_genes_scanpy - feature_annotation - Build and push docker image

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souporcell - genetic_demux - Build and push docker image

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split_modalities - dataflow - Build and push docker image

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multi_star - mapping - Build and push docker image

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samtools - genetic_demux - Build and push docker image

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subset_obsp - filter - Build and push docker image

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sync_test_resources - download - Build and push docker image

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tar_extract - compression - Build and push docker image

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split_h5mu - dataflow - Build and push docker image

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split_h5mu_train_test - dataflow - Build and push docker image

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pad_tokenize - scgpt - Build and push docker image

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svm_annotation - annotate - Build and push docker image

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subset_h5mu - filter - Build and push docker image

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star_align_v273a - mapping - Build and push docker image

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velocyto_to_h5mu - convert - Build and push docker image

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star_align - mapping - Build and push docker image

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tfidf - transform - Build and push docker image

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velocyto - velocity - Build and push docker image

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umap - dimred - Build and push docker image

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tsne - dimred - Build and push docker image

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vireo - genetic_demux - Build and push docker image

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xgboost - labels_transfer - Build and push docker image

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scanvi - annotate - Build and push docker image

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scvelo - velocity - Build and push docker image

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popv - annotate - Build and push docker image

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scarches - integrate - Build and push docker image

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scvi - integrate - Build and push docker image

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totalvi - integrate - Build and push docker image

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onclass - annotate - Build and push docker image

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Cell type annotation: scGPT workflow (#832) #1122

Summary

Cell type annotation: scGPT workflow (#832) #1122

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Run details

main-build.yml

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