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Fix argument default and integration tests after #936 (#938) #7691

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Fix argument default and integration tests after #936 (#938)

Fix argument default and integration tests after #936 (#938) #7691

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Job Run time
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6m 9s
linting
2m 38s
viash_test (cell_type_annotation, scgpt, src/scgpt/cell_type_annotation/config.vsh.yaml, src/scgp...
19m 46s
viash_test (cross_check_genes, scgpt, src/scgpt/cross_check_genes/config.vsh.yaml, src/scgpt/cros...
9m 49s
viash_test (binning, scgpt, src/scgpt/binning/config.vsh.yaml, src/scgpt/binning/, python_script,...
3m 12s
viash_test (pad_tokenize, scgpt, src/scgpt/pad_tokenize/config.vsh.yaml, src/scgpt/pad_tokenize/,...
7m 19s
viash_test (embedding, scgpt, src/scgpt/embedding/config.vsh.yaml, src/scgpt/embedding/, python_s...
32m 52s
viash_test (dsc_pileup, genetic_demux, src/genetic_demux/dsc_pileup/config.vsh.yaml, src/genetic_...
5m 52s
viash_test (scsplit, genetic_demux, src/genetic_demux/scsplit/config.vsh.yaml, src/genetic_demux/...
6m 34s
viash_test (cellsnp, genetic_demux, src/genetic_demux/cellsnp/config.vsh.yaml, src/genetic_demux/...
7m 17s
viash_test (freemuxlet, genetic_demux, src/genetic_demux/freemuxlet/config.vsh.yaml, src/genetic_...
8m 15s
viash_test (bcftools, genetic_demux, src/genetic_demux/bcftools/config.vsh.yaml, src/genetic_demu...
4m 41s
viash_test (demuxlet, genetic_demux, src/genetic_demux/demuxlet/config.vsh.yaml, src/genetic_demu...
9m 9s
viash_test (freebayes, genetic_demux, src/genetic_demux/freebayes/config.vsh.yaml, src/genetic_de...
2m 44s
viash_test (vireo, genetic_demux, src/genetic_demux/vireo/config.vsh.yaml, src/genetic_demux/vire...
2m 29s
viash_test (souporcell, genetic_demux, src/genetic_demux/souporcell/config.vsh.yaml, src/genetic_...
6m 58s
viash_test (samtools, genetic_demux, src/genetic_demux/samtools/config.vsh.yaml, src/genetic_demu...
5m 30s
viash_test (build_cellranger_reference, reference, src/reference/build_cellranger_reference/confi...
6m 44s
viash_test (build_star_reference, reference, src/reference/build_star_reference/config.vsh.yml, s...
7m 15s
viash_test (make_reference, reference, src/reference/make_reference/config.vsh.yaml, src/referenc...
8m 24s
viash_test (build_cellranger_arc_reference, reference, src/reference/build_cellranger_arc_referen...
3m 44s
viash_test (cellranger_mkgtf, reference, src/reference/cellranger_mkgtf/config.vsh.yaml, src/refe...
4m 12s
viash_test (build_bdrhap_reference, reference, src/reference/build_bdrhap_reference/config.vsh.ya...
3m 29s
viash_test (from_h5ad_to_h5mu, convert, src/convert/from_h5ad_to_h5mu/config.vsh.yaml, src/conver...
3m 12s
viash_test (from_10xmtx_to_h5mu, convert, src/convert/from_10xmtx_to_h5mu/config.vsh.yaml, src/co...
3m 23s
viash_test (from_10xh5_to_h5mu, convert, src/convert/from_10xh5_to_h5mu/config.vsh.yaml, src/conv...
3m 47s
viash_test (from_cellranger_multi_to_h5mu, convert, src/convert/from_cellranger_multi_to_h5mu/con...
3m 48s
viash_test (from_h5mu_to_h5ad, convert, src/convert/from_h5mu_to_h5ad/config.vsh.yaml, src/conver...
3m 19s
viash_test (from_h5mu_to_seurat, convert, src/convert/from_h5mu_to_seurat/config.vsh.yaml, src/co...
4m 2s
viash_test (from_bdrhap_to_h5mu, convert, src/convert/from_bdrhap_to_h5mu/config.vsh.yaml, src/co...
3m 8s
viash_test (from_bd_to_10x_molecular_barcode_tags, convert, src/convert/from_bd_to_10x_molecular_...
3m 17s
viash_test (bcl_convert, demux, src/demux/bcl_convert/config.vsh.yaml, src/demux/bcl_convert/, ba...
2m 14s
viash_test (cellranger_mkfastq, demux, src/demux/cellranger_mkfastq/config.vsh.yaml, src/demux/ce...
3m 14s
viash_test (bcl2fastq, demux, src/demux/bcl2fastq/config.vsh.yaml, src/demux/bcl2fastq/, bash_scr...
2m 40s
viash_test (cellranger_atac_mkfastq, demux, src/demux/cellranger_atac_mkfastq/config.vsh.yaml, sr...
3m 57s
viash_test (lianapy, interpret, src/interpret/lianapy/config.vsh.yaml, src/interpret/lianapy/, py...
3m 54s
viash_test (filter_10xh5, process_10xh5, src/process_10xh5/filter_10xh5/config.vsh.yaml, src/proc...
4m 53s
viash_test (scarches, integrate, src/integrate/scarches/config.vsh.yaml, src/integrate/scarches/,...
11m 37s
viash_test (harmonypy, integrate, src/integrate/harmonypy/config.vsh.yaml, src/integrate/harmonyp...
2m 54s
viash_test (scvi, integrate, src/integrate/scvi/config.vsh.yaml, src/integrate/scvi/, python_scri...
8m 40s
viash_test (scanorama, integrate, src/integrate/scanorama/config.vsh.yaml, src/integrate/scanoram...
3m 4s
viash_test (totalvi, integrate, src/integrate/totalvi/config.vsh.yaml, src/integrate/totalvi/, py...
9m 30s
viash_test (filter_with_counts, filter, src/filter/filter_with_counts/config.vsh.yaml, src/filter...
3m 27s
viash_test (subset_obsp, filter, src/filter/subset_obsp/config.vsh.yaml, src/filter/subset_obsp/,...
2m 35s
viash_test (intersect_obs, filter, src/filter/intersect_obs/config.vsh.yaml, src/filter/intersect...
2m 7s
viash_test (remove_modality, filter, src/filter/remove_modality/config.vsh.yaml, src/filter/remov...
2m 37s
viash_test (do_filter, filter, src/filter/do_filter/config.vsh.yaml, src/filter/do_filter/, pytho...
2m 39s
viash_test (subset_h5mu, filter, src/filter/subset_h5mu/config.vsh.yaml, src/filter/subset_h5mu/,...
4m 15s
viash_test (delimit_fraction, filter, src/filter/delimit_fraction/config.vsh.yaml, src/filter/del...
3m 35s
viash_test (filter_with_scrublet, filter, src/filter/filter_with_scrublet/config.vsh.yaml, src/fi...
4m 8s
viash_test (tar_extract, compression, src/compression/tar_extract/config.vsh.yaml, src/compressio...
3m 32s
viash_test (compress_h5mu, compression, src/compression/compress_h5mu/config.vsh.yaml, src/compre...
2m 59s
viash_test (velocyto, velocity, src/velocity/velocyto/config.vsh.yaml, src/velocity/velocyto/, ba...
5m 47s
viash_test (velocyto_to_h5mu, convert, src/velocity/velocyto_to_h5mu/config.vsh.yaml, src/velocit...
4m 0s
viash_test (scvelo, velocity, src/velocity/scvelo/config.vsh.yaml, src/velocity/scvelo/, python_s...
5m 29s
viash_test (cellbender_remove_background_v0_2, correction, src/correction/cellbender_remove_backg...
6m 33s
viash_test (cellbender_remove_background, correction, src/correction/cellbender_remove_background...
9m 45s
viash_test (tsne, dimred, src/dimred/tsne/config.vsh.yaml, src/dimred/tsne/, python_script, dimre...
4m 10s
viash_test (umap, dimred, src/dimred/umap/config.vsh.yaml, src/dimred/umap/, python_script, dimre...
3m 24s
viash_test (lsi, dimred, src/dimred/lsi/config.vsh.yaml, src/dimred/lsi/, python_script, dimred/lsi)
7m 47s
viash_test (pca, dimred, src/dimred/pca/config.vsh.yaml, src/dimred/pca/, python_script, dimred/pca)
3m 16s
viash_test (densmap, dimred, src/dimred/densmap/config.vsh.yaml, src/dimred/densmap/, python_scri...
3m 26s
viash_test (cellxgene_census, query, src/query/cellxgene_census/config.vsh.yaml, src/query/cellxg...
3m 39s
viash_test (publish, transfer, src/transfer/publish/config.vsh.yaml, src/transfer/publish/, bash_...
2m 0s
viash_test (find_neighbors, neighbors, src/neighbors/find_neighbors/config.vsh.yaml, src/neighbor...
3m 48s
viash_test (bbknn, neighbors, src/neighbors/bbknn/config.vsh.yaml, src/neighbors/bbknn/, python_s...
4m 16s
viash_test (multiqc, qc, src/qc/multiqc/config.vsh.yaml, src/qc/multiqc/, python_script, qc/multiqc)
2m 52s
viash_test (fastqc, qc, src/qc/fastqc/config.vsh.yaml, src/qc/fastqc/, bash_script, qc/fastqc)
3m 36s
viash_test (calculate_atac_qc_metrics, qc, src/qc/calculate_atac_qc_metrics/config.vsh.yaml, src/...
3m 50s
viash_test (calculate_qc_metrics, qc, src/qc/calculate_qc_metrics/config.vsh.yaml, src/qc/calcula...
9m 59s
viash_test (cellranger_atac_count, mapping, src/mapping/cellranger_atac_count/config.vsh.yaml, sr...
13m 43s
viash_test (htseq_count_to_h5mu, mapping, src/mapping/htseq_count_to_h5mu/config.vsh.yaml, src/ma...
2m 49s
viash_test (star_align_v273a, mapping, src/mapping/star_align_v273a/config.vsh.yaml, src/mapping/...
9m 12s
viash_test (htseq_count, mapping, src/mapping/htseq_count/config.vsh.yaml, src/mapping/htseq_coun...
3m 55s
viash_test (cellranger_multi, mapping, src/mapping/cellranger_multi/config.vsh.yaml, src/mapping/...
31m 7s
viash_test (star_align, mapping, src/mapping/star_align/config.vsh.yaml, src/mapping/star_align/,...
8m 35s
viash_test (samtools_sort, mapping, src/mapping/samtools_sort/config.vsh.yaml, src/mapping/samtoo...
2m 30s
viash_test (bd_rhapsody, mapping, src/mapping/bd_rhapsody/config.vsh.yaml, src/mapping/bd_rhapsod...
10m 41s
viash_test (cellranger_count, mapping, src/mapping/cellranger_count/config.vsh.yaml, src/mapping/...
13m 2s
viash_test (multi_star_to_h5mu, mapping, src/mapping/multi_star_to_h5mu/config.vsh.yaml, src/mapp...
2m 51s
viash_test (multi_star, mapping, src/mapping/multi_star/config.vsh.yaml, src/mapping/multi_star/,...
12m 1s
viash_test (cellranger_count_split, mapping, src/mapping/cellranger_count_split/config.vsh.yaml, ...
2m 9s
viash_test (clr, transform, src/transform/clr/config.vsh.yaml, src/transform/clr/, python_script,...
3m 3s
viash_test (log1p, transform, src/transform/log1p/config.vsh.yaml, src/transform/log1p/, python_s...
2m 54s
viash_test (normalize_total, transform, src/transform/normalize_total/config.vsh.yaml, src/transf...
2m 46s
viash_test (move_layer, transform, src/transform/move_layer/config.vsh.yaml, src/transform/move_l...
3m 26s
viash_test (delete_layer, transform, src/transform/delete_layer/config.vsh.yaml, src/transform/de...
4m 21s
viash_test (bpcells_regress_out, transform, src/transform/bpcells_regress_out/config.vsh.yaml, sr...
10m 22s
viash_test (regress_out, transform, src/transform/regress_out/config.vsh.yaml, src/transform/regr...
3m 52s
viash_test (tfidf, transform, src/transform/tfidf/config.vsh.yaml, src/transform/tfidf/, python_s...
3m 56s
viash_test (scale, transform, src/transform/scale/config.vsh.yaml, src/transform/scale/, python_s...
4m 2s
viash_test (split_modalities, dataflow, src/dataflow/split_modalities/config.vsh.yaml, src/datafl...
2m 56s
viash_test (split_h5mu, dataflow, src/dataflow/split_h5mu/config.vsh.yaml, src/dataflow/split_h5m...
3m 14s
viash_test (split_h5mu_train_test, dataflow, src/dataflow/split_h5mu_train_test/config.vsh.yaml, ...
5m 1s
viash_test (merge, dataflow, src/dataflow/merge/config.vsh.yml, src/dataflow/merge/, python_scrip...
3m 20s
viash_test (concatenate_h5mu, dataflow, src/dataflow/concatenate_h5mu/config.vsh.yaml, src/datafl...
4m 0s
viash_test (make_params, files, src/files/make_params/config.vsh.yaml, src/files/make_params/, r_...
4m 55s
viash_test (mermaid, report, src/report/mermaid/config.vsh.yaml, src/report/mermaid/, bash_script...
3m 9s
viash_test (join_csv, metadata, src/metadata/join_csv/config.vsh.yml, src/metadata/join_csv/, pyt...
4m 1s
viash_test (move_obsm_to_obs, metadata, src/metadata/move_obsm_to_obs/config.vsh.yaml, src/metada...
2m 36s
viash_test (join_uns_to_obs, metadata, src/metadata/join_uns_to_obs/config.vsh.yml, src/metadata/...
3m 2s
viash_test (grep_annotation_column, metadata, src/metadata/grep_annotation_column/config.vsh.yaml...
2m 43s
viash_test (duplicate_obs, metadata, src/metadata/duplicate_obs/config.vsh.yaml, src/metadata/dup...
2m 52s
viash_test (add_id, metadata, src/metadata/add_id/config.vsh.yaml, src/metadata/add_id/, python_s...
3m 10s
viash_test (duplicate_var, metadata, src/metadata/duplicate_var/config.vsh.yaml, src/metadata/dup...
2m 40s
viash_test (xgboost, labels_transfer, src/labels_transfer/xgboost/config.vsh.yaml, src/labels_tra...
3m 15s
viash_test (knn, labels_transfer, src/labels_transfer/knn/config.vsh.yaml, src/labels_transfer/kn...
7m 29s
viash_test (download_file, download, src/download/download_file/config.vsh.yaml, src/download/dow...
3m 9s
viash_test (sync_test_resources, download, src/download/sync_test_resources/config.vsh.yaml, src/...
3m 15s
viash_test (leiden, cluster, src/cluster/leiden/config.vsh.yaml, src/cluster/leiden/, python_scri...
4m 9s
viash_test (scanvi, annotate, src/annotate/scanvi/config.vsh.yaml, src/annotate/scanvi/, python_s...
9m 11s
viash_test (popv, annotate, src/annotate/popv/config.vsh.yaml, src/annotate/popv/, python_script,...
8m 53s
viash_test (random_forest_annotation, annotate, src/annotate/random_forest_annotation/config.vsh....
3m 53s
viash_test (onclass, annotate, src/annotate/onclass/config.vsh.yaml, src/annotate/onclass/, pytho...
9m 53s
viash_test (celltypist, annotate, src/annotate/celltypist/config.vsh.yaml, src/annotate/celltypis...
3m 36s
viash_test (svm_annotation, annotate, src/annotate/svm_annotation/config.vsh.yaml, src/annotate/s...
3m 19s
viash_test (score_genes_cell_cycle_scanpy, feature_annotation, src/feature_annotation/score_genes...
3m 11s
viash_test (highly_variable_features_scanpy, feature_annotation, src/feature_annotation/highly_va...
3m 10s
viash_test (score_genes_scanpy, feature_annotation, src/feature_annotation/score_genes_scanpy/con...
6m 9s
10h 50m 34s