openpipelines-bio / openpipeline

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Refactor components to use new Viash version >= 0.9.0 #776

Open jakubmajercik opened 1 month ago

jakubmajercik commented 1 month ago

Refactor component configs:

Branched out from main and develop - certain new components might not be included

Namespace checklist:

Namespace checklist - [x] annotate - [x] cluster - [x] compression - [x] compress_h5mu - ERROR meta path - [x] tar_extract - [x] convert - [x] from_10xh5_to_h5mu - [x] from_10xmtx_to_h5mu - [x] from_bdrhap_to_h5mu - [x] from_bd_to_10x_molecular_barcode_tags - [x] from_cellranger_multi_to_h5mu - [x] from_h5ad_to_h5mu - [x] from_h5mu_to_h5ad - [x] from_h5mu_to_seurat - [x] correction - [x] cellbender_remove_background - [x] cellbender_remove_background_v0_2 - [x] dataflow - [x] concat - [x] concatenate_h5mu - [x] merge - [x] split_modalities - [x] demux - [x] bcl2fastq - [x] bcl_convert - [x] cellranger_mkfastq - [x] dimred - [x] pca - [x] umap - [x] tsne - [x] download - [x] download_file - [x] sync_test_resources - [x] feature_annotation - [x] highly_variable_features_scanpy - [x] score_genes_cell_cycle_scanpy - [x] score_genes_scanpy - [x] files - [x] filter - [x] delimit_fraction - [x] do_filter - [x] filter_with_counts - [x] filter_with_hvg - deprecated status - [x] filter_with_scrublet - [x] intersect_obs - [x] remove_modality - [x] subset_h5mu - [x] genetic_demux - [x] bcftools - [x] cellsnp - [x] demuxlet - [x] dsc_pileup - [x] freebayes - [x] freemuxlet - [x] samtools - [x] scsplit - [x] souporcell - [x] vireo - [x] integrate - [x] harmony - [x] harmonypy - [x] scanorama - [x] scarches - [x] scvi - [x] totalvi - [ ] interactive - issue with `docker_run_args` - [ ] run_cellxgene `Error: Dataset does not have an allowed type.` - [ ] run_cirrocumulus - no port specified - [x] interpret - [x] labels_transfer - [x] knn - [x] xgboost - [x] mapping - [x] bd_rhapsody - [x] cellranger_count - [x] cellranger_count_split - [x] cellranger_multi - [x] htseq_count - [x] htseq_count_to_h5mu - [x] multi_star - [x] multi_star_to_h5mu - [x] samtools_sort - [x] star_align - [x] star_align_v273a - [x] star_build_reference - [x] metadata - [x] add_id - [x] grep_annotation_column - removed `float16`! apparently it is not supported sparse matrix dtype. test fails otherwise - [x] join_csv - [x] join_uns_to_obs - [x] move_obsm_to_obs - [x] neighbors - [x] bbknn - [x] find_neighbors - [x] process_10xh5 - [x] qc - [x] calculate_qc_metrics - [x] fastqc - [x] multiqc - [x] query - [x] reference - [x] build_bdrhap_reference - [x] build_cellranger_reference - [x] make_reference - [x] report - [x] transfer - [x] transform - [x] clr - [x] delete_layer - [x] log1p - [x] move_layer - [x] normalize_total - [x] regress_out - [x] scaling - [x] velocity - [x] scvelo - [x] velocyto - [x] velocyto_to_h5mu