diff --git a/CHANGELOG.md b/CHANGELOG.md index d9b97527d14..b8908e2f198 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,10 @@ * Removed `split_h5mu_train_test` component (PR #1020). +* `compress_h5mu`: rename `compression` argument to `output_compression` (PR #1017, PR #1018). + +* `delimit_fraction`: remove unused `layer` argument (PR #1018). + ## MAJOR CHANGES * `mapping/cellranger_*`: Upgrade CellRanger to v9.0 (PR #992 and #1006). @@ -14,6 +18,8 @@ * Move output file compression argument for AnnData and MuData files to a base config file (`src/base/h5_compression_argument.yaml`) (PR #1017). +* Add missing descriptions to components and arguments (PR #1018). + ## BUG FIXES * Bump viash to 0.9.4. This adds support for nextflow versions starting major version 25.01 and fixes an issue where an integer being passed to a argument with `type: double` resulted in an error (PR #1016). diff --git a/src/annotate/scanvi/config.vsh.yaml b/src/annotate/scanvi/config.vsh.yaml index 96b22e15779..62e0ac3bf33 100644 --- a/src/annotate/scanvi/config.vsh.yaml +++ b/src/annotate/scanvi/config.vsh.yaml @@ -21,6 +21,8 @@ argument_groups: direction: input required: true - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/annotate/svm_annotation/config.vsh.yaml b/src/annotate/svm_annotation/config.vsh.yaml index e826e586f72..1996bd628b3 100644 --- a/src/annotate/svm_annotation/config.vsh.yaml +++ b/src/annotate/svm_annotation/config.vsh.yaml @@ -52,6 +52,9 @@ argument_groups: type: string description: required: true + description: | + Key in .obs attribute of reference modality with cell-type information. + - name: "--reference_var_gene_names" type: string required: false diff --git a/src/cluster/leiden/config.vsh.yaml b/src/cluster/leiden/config.vsh.yaml index 36fa0ec5725..99c868a04af 100644 --- a/src/cluster/leiden/config.vsh.yaml +++ b/src/cluster/leiden/config.vsh.yaml @@ -24,6 +24,8 @@ arguments: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/compression/compress_h5mu/config.vsh.yaml b/src/compression/compress_h5mu/config.vsh.yaml index de5553f04c4..eeb72165fba 100644 --- a/src/compression/compress_h5mu/config.vsh.yaml +++ b/src/compression/compress_h5mu/config.vsh.yaml @@ -18,12 +18,7 @@ arguments: description: location of output file. required: true direction: output - - name: "--compression" - type: string - description: Compression type. - required: false - default: "gzip" - choices: ["lzf", "gzip"] +__merge__: [., /src/base/h5_compression_argument.yaml] resources: - type: python_script path: script.py diff --git a/src/compression/compress_h5mu/run_test.py b/src/compression/compress_h5mu/run_test.py index 09f864130c9..b89ce9afdb2 100644 --- a/src/compression/compress_h5mu/run_test.py +++ b/src/compression/compress_h5mu/run_test.py @@ -35,7 +35,7 @@ def test_compress_h5mu(run_component, tmp_path, compression_type): str(input_file), "--output", str(output_file), - "--compression", + "--output_compression", compression_type, ] ) diff --git a/src/compression/compress_h5mu/script.py b/src/compression/compress_h5mu/script.py index 7e6292d9e78..d65408be9e4 100644 --- a/src/compression/compress_h5mu/script.py +++ b/src/compression/compress_h5mu/script.py @@ -13,4 +13,4 @@ from compress_h5mu import compress_h5mu if __name__ == "__main__": - compress_h5mu(par["input"], par["output"], compression=par["compression"]) + compress_h5mu(par["input"], par["output"], compression=par["output_compression"]) diff --git a/src/convert/from_h5ad_to_h5mu/config.vsh.yaml b/src/convert/from_h5ad_to_h5mu/config.vsh.yaml index 1a40dda84c8..51645f1a77c 100644 --- a/src/convert/from_h5ad_to_h5mu/config.vsh.yaml +++ b/src/convert/from_h5ad_to_h5mu/config.vsh.yaml @@ -15,6 +15,9 @@ arguments: required: true multiple: true - name: "--modality" + description: | + List of names to use for the modalities. Will be used as the keys in the .mod attribute in the output MuData object + The number of items provided for this argument equal the number of input files (--input) and their order should match. type: string default: "rna" required: false diff --git a/src/convert/from_h5mu_to_h5ad/config.vsh.yaml b/src/convert/from_h5mu_to_h5ad/config.vsh.yaml index 111d9af4d30..962f914d964 100644 --- a/src/convert/from_h5mu_to_h5ad/config.vsh.yaml +++ b/src/convert/from_h5mu_to_h5ad/config.vsh.yaml @@ -14,6 +14,8 @@ arguments: direction: input required: true - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/correction/cellbender_remove_background/config.vsh.yaml b/src/correction/cellbender_remove_background/config.vsh.yaml index 3b06f13452a..c354834d01a 100644 --- a/src/correction/cellbender_remove_background/config.vsh.yaml +++ b/src/correction/cellbender_remove_background/config.vsh.yaml @@ -46,6 +46,8 @@ argument_groups: type: string default: "cellbender_cell_size" - name: "--obs_droplet_efficiency" + description: | + Name of the column in the .obs dataframe to store the droplet efficiencies in. type: string default: "cellbender_droplet_efficiency" - name: "--obs_latent_scale" diff --git a/src/dataflow/concatenate_h5mu/config.vsh.yaml b/src/dataflow/concatenate_h5mu/config.vsh.yaml index 899576a99ea..75756bcd12c 100644 --- a/src/dataflow/concatenate_h5mu/config.vsh.yaml +++ b/src/dataflow/concatenate_h5mu/config.vsh.yaml @@ -27,6 +27,8 @@ arguments: If specified, must be of same length as `--input`. required: false - name: "--output" + description: | + Output location for the concatenated MuData object file. alternatives: ["-o"] type: file direction: output diff --git a/src/dataflow/split_h5mu/config.vsh.yaml b/src/dataflow/split_h5mu/config.vsh.yaml index 2497ac6579b..b80d01fbfe9 100644 --- a/src/dataflow/split_h5mu/config.vsh.yaml +++ b/src/dataflow/split_h5mu/config.vsh.yaml @@ -13,6 +13,8 @@ argument_groups: description: Path to a single .h5mu file. required: true - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/demux/bcl2fastq/config.vsh.yaml b/src/demux/bcl2fastq/config.vsh.yaml index 85524ff99bb..3bce5bf76e5 100644 --- a/src/demux/bcl2fastq/config.vsh.yaml +++ b/src/demux/bcl2fastq/config.vsh.yaml @@ -32,6 +32,9 @@ arguments: description: Reports directory example: reports_dir - name: "--ignore_missing" + description: | + Interpret missing *.bcl files as no call (N), interpret missing control files as not-set + control bits and fill in with zeros when *.stats files are missing. type: boolean_true resources: - type: bash_script diff --git a/src/dimred/densmap/config.vsh.yaml b/src/dimred/densmap/config.vsh.yaml index db2f6749215..9f23a22a3f2 100644 --- a/src/dimred/densmap/config.vsh.yaml +++ b/src/dimred/densmap/config.vsh.yaml @@ -17,6 +17,8 @@ argument_groups: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/dimred/pca/config.vsh.yaml b/src/dimred/pca/config.vsh.yaml index b99d4fe4de1..84c4165ba27 100644 --- a/src/dimred/pca/config.vsh.yaml +++ b/src/dimred/pca/config.vsh.yaml @@ -16,6 +16,8 @@ arguments: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/dimred/tsne/config.vsh.yaml b/src/dimred/tsne/config.vsh.yaml index 5a8a0549304..9f3f200179d 100644 --- a/src/dimred/tsne/config.vsh.yaml +++ b/src/dimred/tsne/config.vsh.yaml @@ -16,6 +16,8 @@ argument_groups: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: true diff --git a/src/dimred/umap/config.vsh.yaml b/src/dimred/umap/config.vsh.yaml index 3598d4a84d4..3fe11628342 100644 --- a/src/dimred/umap/config.vsh.yaml +++ b/src/dimred/umap/config.vsh.yaml @@ -16,6 +16,8 @@ argument_groups: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml b/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml index 2408280c141..27c165187f3 100644 --- a/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml +++ b/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml @@ -25,6 +25,8 @@ arguments: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml b/src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml index 6412e18f9b9..d84c25cc78b 100644 --- a/src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml +++ b/src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml @@ -20,6 +20,8 @@ argument_groups: required: true example: input_file.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/feature_annotation/score_genes_scanpy/config.vsh.yaml b/src/feature_annotation/score_genes_scanpy/config.vsh.yaml index d1b9b846ff4..108fbf1dfc5 100644 --- a/src/feature_annotation/score_genes_scanpy/config.vsh.yaml +++ b/src/feature_annotation/score_genes_scanpy/config.vsh.yaml @@ -49,6 +49,8 @@ argument_groups: required: false example: gene_pool.txt - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/filter/delimit_fraction/config.vsh.yaml b/src/filter/delimit_fraction/config.vsh.yaml index 61a661c677e..37fe7adc974 100644 --- a/src/filter/delimit_fraction/config.vsh.yaml +++ b/src/filter/delimit_fraction/config.vsh.yaml @@ -17,15 +17,12 @@ argument_groups: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false - - name: "--layer" - type: string - example: "raw_counts" - required: false - - name: "--obs_fraction_column" type: string required: true diff --git a/src/filter/do_filter/config.vsh.yaml b/src/filter/do_filter/config.vsh.yaml index c00db5dcbd9..5be48732885 100644 --- a/src/filter/do_filter/config.vsh.yaml +++ b/src/filter/do_filter/config.vsh.yaml @@ -15,6 +15,8 @@ arguments: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/filter/filter_with_counts/config.vsh.yaml b/src/filter/filter_with_counts/config.vsh.yaml index 2ecb04408ed..c717481a775 100644 --- a/src/filter/filter_with_counts/config.vsh.yaml +++ b/src/filter/filter_with_counts/config.vsh.yaml @@ -21,11 +21,17 @@ argument_groups: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false - name: "--layer" + description: | + description: | + Location of the count matrix. If specified, will be used to select a key from .layers, + otherwise .X is used. type: string example: "raw_counts" required: false diff --git a/src/filter/filter_with_scrublet/config.vsh.yaml b/src/filter/filter_with_scrublet/config.vsh.yaml index f7257800359..00b96c590a0 100644 --- a/src/filter/filter_with_scrublet/config.vsh.yaml +++ b/src/filter/filter_with_scrublet/config.vsh.yaml @@ -36,6 +36,8 @@ arguments: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/filter/intersect_obs/config.vsh.yaml b/src/filter/intersect_obs/config.vsh.yaml index 6e99109bbd5..43a885707ff 100644 --- a/src/filter/intersect_obs/config.vsh.yaml +++ b/src/filter/intersect_obs/config.vsh.yaml @@ -19,6 +19,8 @@ arguments: example: input.h5mu - name: "--modalities" + description: | + Which modalities from the input MuData file to process. type: string multiple: true required: true diff --git a/src/filter/remove_modality/config.vsh.yaml b/src/filter/remove_modality/config.vsh.yaml index 42a5f4e339e..c3427766fd4 100644 --- a/src/filter/remove_modality/config.vsh.yaml +++ b/src/filter/remove_modality/config.vsh.yaml @@ -13,6 +13,8 @@ arguments: required: true example: input.h5mu - name: "--modality" + description: | + Name(s) of the modality to remove type: string multiple: true required: true diff --git a/src/filter/subset_h5mu/config.vsh.yaml b/src/filter/subset_h5mu/config.vsh.yaml index 11f7473d91a..5b84abe6e96 100644 --- a/src/filter/subset_h5mu/config.vsh.yaml +++ b/src/filter/subset_h5mu/config.vsh.yaml @@ -13,6 +13,8 @@ arguments: required: true example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/filter/subset_obsp/config.vsh.yaml b/src/filter/subset_obsp/config.vsh.yaml index 2eb2c272bde..c2d3ae13cd3 100644 --- a/src/filter/subset_obsp/config.vsh.yaml +++ b/src/filter/subset_obsp/config.vsh.yaml @@ -15,6 +15,8 @@ argument_groups: required: true example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/integrate/harmonypy/config.vsh.yaml b/src/integrate/harmonypy/config.vsh.yaml index 78eee42b131..23e6ea98ffd 100644 --- a/src/integrate/harmonypy/config.vsh.yaml +++ b/src/integrate/harmonypy/config.vsh.yaml @@ -21,6 +21,8 @@ arguments: direction: output required: true - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/integrate/scanorama/config.vsh.yaml b/src/integrate/scanorama/config.vsh.yaml index e8c1d990d83..54723344c53 100644 --- a/src/integrate/scanorama/config.vsh.yaml +++ b/src/integrate/scanorama/config.vsh.yaml @@ -15,6 +15,8 @@ arguments: direction: input required: true - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/integrate/scarches/config.vsh.yaml b/src/integrate/scarches/config.vsh.yaml index d5c6d2953d1..fd3480bcd6e 100644 --- a/src/integrate/scarches/config.vsh.yaml +++ b/src/integrate/scarches/config.vsh.yaml @@ -21,6 +21,8 @@ argument_groups: description: Layer to be used for scArches, if .X is not to be used. required: false - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/integrate/scvi/config.vsh.yaml b/src/integrate/scvi/config.vsh.yaml index f3cef372030..7f9c25c441b 100644 --- a/src/integrate/scvi/config.vsh.yaml +++ b/src/integrate/scvi/config.vsh.yaml @@ -18,6 +18,8 @@ argument_groups: direction: input required: true - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/interpret/lianapy/config.vsh.yaml b/src/interpret/lianapy/config.vsh.yaml index 352b02a5c35..48907bfdf99 100644 --- a/src/interpret/lianapy/config.vsh.yaml +++ b/src/interpret/lianapy/config.vsh.yaml @@ -20,6 +20,8 @@ arguments: direction: output required: true - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/mapping/bd_rhapsody/config.vsh.yaml b/src/mapping/bd_rhapsody/config.vsh.yaml index 62b50b2c8f8..f786a5f727e 100644 --- a/src/mapping/bd_rhapsody/config.vsh.yaml +++ b/src/mapping/bd_rhapsody/config.vsh.yaml @@ -620,6 +620,8 @@ argument_groups: info: config_key: VDJ_VGene_Evalue - name: --write_filtered_reads + description: + Output processed FASTQ reads. type: boolean multiple: false info: diff --git a/src/mapping/cellranger_count_split/config.vsh.yaml b/src/mapping/cellranger_count_split/config.vsh.yaml index d0cd23a31e0..2bec7ef1c28 100644 --- a/src/mapping/cellranger_count_split/config.vsh.yaml +++ b/src/mapping/cellranger_count_split/config.vsh.yaml @@ -15,36 +15,43 @@ arguments: example: input_dir description: Output directory from a Cell Ranger count run. - name: --filtered_h5 + description: | + Output path for the h5 file storing the filtered counts. type: file direction: output required: false - # description: Counts in AnnData format. example: filtered_feature_bc_matrix.h5 - name: --metrics_summary + description: | + Where to store the 'metrics_summary' CSV file. type: file direction: output required: false - # description: Counts in AnnData format. example: metrics_summary.csv - name: --molecule_info + description: | + Where to store Cell Ranger's 'molecule_info.h5' file. type: file direction: output required: false - # description: Counts in AnnData format. example: molecule_info.h5 - name: --bam + description: | + Location of output BAM files. type: file direction: output required: false - # description: Counts in AnnData format. example: possorted_genome_bam.bam - name: --bai + description: | + Where to store the BAM index files. type: file direction: output required: false - # description: Counts in AnnData format. example: possorted_genome_bam.bam.bai - name: --raw_h5 + description: | + Output path for the h5 file storing the raw counts. type: file direction: output required: false diff --git a/src/metadata/add_id/config.vsh.yaml b/src/metadata/add_id/config.vsh.yaml index 6c99bbd929e..f16c33f35dc 100644 --- a/src/metadata/add_id/config.vsh.yaml +++ b/src/metadata/add_id/config.vsh.yaml @@ -23,6 +23,8 @@ arguments: description: "Name of the .obs column where to store the id." default: "sample_id" - name: "--output" + description: | + Name of output MuData file. alternatives: ["-o"] type: file direction: output diff --git a/src/metadata/grep_annotation_column/config.vsh.yaml b/src/metadata/grep_annotation_column/config.vsh.yaml index 38d0c368796..f9a9c1e7097 100644 --- a/src/metadata/grep_annotation_column/config.vsh.yaml +++ b/src/metadata/grep_annotation_column/config.vsh.yaml @@ -41,6 +41,8 @@ argument_groups: description: Arguments related to how the output will be written. arguments: - name: "--output" + description: | + Location of the output MuData file. alternatives: ["-o"] type: file direction: output diff --git a/src/metadata/join_csv/config.vsh.yml b/src/metadata/join_csv/config.vsh.yml index ae478be0e55..ddd3ef0830e 100644 --- a/src/metadata/join_csv/config.vsh.yml +++ b/src/metadata/join_csv/config.vsh.yml @@ -15,6 +15,8 @@ argument_groups: required: true example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/metadata/join_uns_to_obs/config.vsh.yml b/src/metadata/join_uns_to_obs/config.vsh.yml index 5c225838fe7..e0c5a68ed51 100644 --- a/src/metadata/join_uns_to_obs/config.vsh.yml +++ b/src/metadata/join_uns_to_obs/config.vsh.yml @@ -10,10 +10,14 @@ arguments: required: true example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false - name: "--uns_key" + description: | + Lookup key from .uns pointing to the input data. type: string required: true - name: "--output" diff --git a/src/metadata/move_obsm_to_obs/config.vsh.yaml b/src/metadata/move_obsm_to_obs/config.vsh.yaml index 6ebf61fec02..dcbe2318712 100644 --- a/src/metadata/move_obsm_to_obs/config.vsh.yaml +++ b/src/metadata/move_obsm_to_obs/config.vsh.yaml @@ -18,6 +18,8 @@ argument_groups: required: true example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/neighbors/bbknn/config.vsh.yaml b/src/neighbors/bbknn/config.vsh.yaml index d2fa1f618db..ada23d8158f 100644 --- a/src/neighbors/bbknn/config.vsh.yaml +++ b/src/neighbors/bbknn/config.vsh.yaml @@ -16,6 +16,8 @@ arguments: direction: input required: true - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/neighbors/find_neighbors/config.vsh.yaml b/src/neighbors/find_neighbors/config.vsh.yaml index 004fa4bc746..3e4dfe9fe78 100644 --- a/src/neighbors/find_neighbors/config.vsh.yaml +++ b/src/neighbors/find_neighbors/config.vsh.yaml @@ -20,6 +20,8 @@ arguments: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/qc/calculate_atac_qc_metrics/config.vsh.yaml b/src/qc/calculate_atac_qc_metrics/config.vsh.yaml index 6ed683e0436..b3b8d645e74 100644 --- a/src/qc/calculate_atac_qc_metrics/config.vsh.yaml +++ b/src/qc/calculate_atac_qc_metrics/config.vsh.yaml @@ -31,6 +31,8 @@ argument_groups: required: false example: fragments.tsv.gz - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "atac" required: false diff --git a/src/qc/calculate_qc_metrics/config.vsh.yaml b/src/qc/calculate_qc_metrics/config.vsh.yaml index 27659f42a6d..8c0ae77c145 100644 --- a/src/qc/calculate_qc_metrics/config.vsh.yaml +++ b/src/qc/calculate_qc_metrics/config.vsh.yaml @@ -32,10 +32,14 @@ argument_groups: required: true example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false - name: "--layer" + description: | + Layer from modality to use as input data. If not provided the .X attribute is used. type: string example: "raw_counts" required: false diff --git a/src/scgpt/binning/config.vsh.yaml b/src/scgpt/binning/config.vsh.yaml index 8f6189f562c..7b6caced379 100644 --- a/src/scgpt/binning/config.vsh.yaml +++ b/src/scgpt/binning/config.vsh.yaml @@ -21,6 +21,8 @@ argument_groups: description: | Input h5mu file. - name: "--modality" + description: + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/scgpt/cell_type_annotation/config.vsh.yaml b/src/scgpt/cell_type_annotation/config.vsh.yaml index 0a23f777fe0..07806b36abd 100644 --- a/src/scgpt/cell_type_annotation/config.vsh.yaml +++ b/src/scgpt/cell_type_annotation/config.vsh.yaml @@ -50,6 +50,8 @@ argument_groups: description: | The input h5mu file containing of data that have been pre-processed (normalized, binned, genes cross-checked and tokenized). - name: "--modality" + description: + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/scgpt/embedding/config.vsh.yaml b/src/scgpt/embedding/config.vsh.yaml index 2e2623d5bbb..20d214b7983 100644 --- a/src/scgpt/embedding/config.vsh.yaml +++ b/src/scgpt/embedding/config.vsh.yaml @@ -20,6 +20,9 @@ argument_groups: description: | The input h5mu file containing tokenized gene and count data. - name: "--modality" + description: | + Which modality from the input MuData file to process. + type: string default: "rna" required: false diff --git a/src/scgpt/pad_tokenize/config.vsh.yaml b/src/scgpt/pad_tokenize/config.vsh.yaml index 031cb7d7284..6a5498f3980 100644 --- a/src/scgpt/pad_tokenize/config.vsh.yaml +++ b/src/scgpt/pad_tokenize/config.vsh.yaml @@ -21,6 +21,8 @@ argument_groups: description: | The input h5mu file of pre-processed data. - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/transform/clr/config.vsh.yaml b/src/transform/clr/config.vsh.yaml index 4f3f1ae6b43..e2aac00da13 100644 --- a/src/transform/clr/config.vsh.yaml +++ b/src/transform/clr/config.vsh.yaml @@ -14,6 +14,8 @@ arguments: required: true example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "prot" required: false diff --git a/src/transform/delete_layer/config.vsh.yaml b/src/transform/delete_layer/config.vsh.yaml index 8ed18989f43..cb932d81b8c 100644 --- a/src/transform/delete_layer/config.vsh.yaml +++ b/src/transform/delete_layer/config.vsh.yaml @@ -14,6 +14,8 @@ arguments: required: true example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/transform/log1p/config.vsh.yaml b/src/transform/log1p/config.vsh.yaml index 431df95a10a..329fc3b9956 100644 --- a/src/transform/log1p/config.vsh.yaml +++ b/src/transform/log1p/config.vsh.yaml @@ -18,6 +18,8 @@ arguments: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false @@ -43,6 +45,8 @@ arguments: # arguments - name: "--base" + description: | + Base of the logarithm. Natural logarithm is used by default. type: double example: 2 diff --git a/src/transform/move_layer/config.vsh.yaml b/src/transform/move_layer/config.vsh.yaml index a5a2ba0802a..e39e437c984 100644 --- a/src/transform/move_layer/config.vsh.yaml +++ b/src/transform/move_layer/config.vsh.yaml @@ -10,10 +10,15 @@ arguments: required: true example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false - name: "--input_layer" + description: | + Input layer to move to a new output location. If specified, will be used to select a key from .layers, + otherwise .X is used. type: string required: false - name: "--output" @@ -24,6 +29,9 @@ arguments: required: true example: output.h5mu - name: "--output_layer" + description: | + Destination location for the layer. If not provided, .X will be used, + Otherwise, will be the key for the .layers attribute in the output MuData file. type: string required: false __merge__: [., /src/base/h5_compression_argument.yaml] diff --git a/src/transform/normalize_total/config.vsh.yaml b/src/transform/normalize_total/config.vsh.yaml index 14bdef92bb0..f5e47ec8ce2 100644 --- a/src/transform/normalize_total/config.vsh.yaml +++ b/src/transform/normalize_total/config.vsh.yaml @@ -22,6 +22,8 @@ arguments: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/transform/tfidf/config.vsh.yaml b/src/transform/tfidf/config.vsh.yaml index 912b52eb5e3..17b29567cc6 100644 --- a/src/transform/tfidf/config.vsh.yaml +++ b/src/transform/tfidf/config.vsh.yaml @@ -21,6 +21,8 @@ arguments: example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "atac" required: false diff --git a/src/velocity/scvelo/config.vsh.yaml b/src/velocity/scvelo/config.vsh.yaml index 72082117e88..5672d325fbc 100644 --- a/src/velocity/scvelo/config.vsh.yaml +++ b/src/velocity/scvelo/config.vsh.yaml @@ -20,14 +20,23 @@ argument_groups: required: true type: string - name: "--layer_spliced" + description: | + Name of the layer to store the spliced abundances in. Will be used as key in the .layer attribute of the + output MuData object. type: string required: false default: "spliced" - name: "--layer_unspliced" + description: | + Name of the layer to store the unspliced abundances in. + Will be used as key in the .layer attribute of the output MuData object. type: string required: false default: "unspliced" - name: "--layer_ambiguous" + description: | + Name of the layer to store the abundances in for which no fate was determined. + Will be used as key in the .layer attribute of the output MuData object. type: string required: false default: "ambiguous" diff --git a/src/workflows/annotation/scgpt_annotation/config.vsh.yaml b/src/workflows/annotation/scgpt_annotation/config.vsh.yaml index 3868cf27d0b..66edf03cb35 100644 --- a/src/workflows/annotation/scgpt_annotation/config.vsh.yaml +++ b/src/workflows/annotation/scgpt_annotation/config.vsh.yaml @@ -37,6 +37,8 @@ argument_groups: description: Path to the input file. example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/workflows/integration/scgpt_leiden/config.vsh.yaml b/src/workflows/integration/scgpt_leiden/config.vsh.yaml index 9fdb5bd6210..b136846bf41 100644 --- a/src/workflows/integration/scgpt_leiden/config.vsh.yaml +++ b/src/workflows/integration/scgpt_leiden/config.vsh.yaml @@ -24,6 +24,8 @@ argument_groups: description: Path to the input file. example: input.h5mu - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false diff --git a/src/workflows/multiomics/split_h5mu/config.vsh.yaml b/src/workflows/multiomics/split_h5mu/config.vsh.yaml index 42038adc699..c79ad081ef2 100644 --- a/src/workflows/multiomics/split_h5mu/config.vsh.yaml +++ b/src/workflows/multiomics/split_h5mu/config.vsh.yaml @@ -16,6 +16,8 @@ argument_groups: description: Path to a single .h5mu file. required: true - name: "--modality" + description: | + Which modality from the input MuData file to process. type: string default: "rna" required: false