mecfs_bio.build_system.task

Task objects are where the "real work" of the build system is encapsulated. A Task encodes instructions for how to materialize a given asset. These instructions may include requesting that the build system materialize any dependencies the asset has.

Modules:

• assign_rsids_via_snp151_task –

  Assign RSIDs to variants via joining a database file. Only works for single-nucleotide variations.

• base_task –

  Instructions for materializing an asset.

• combine_gene_lists_task –

  Task to combine gene lists from multiple sources

• compressed_csv_to_parquet_task –

  Enable efficient SQL operations by converting CSV to parquet.

• concat_frames_in_dir_task –

  Concatenate dataframes in a DirectoryAsset to create a single FileAsset.

• concat_frames_task –

  Task to combine the results of multiple Tasks, each of which produces a dataframe.

• consolidate_ld_scores_task –

  Task to read LD scores in the standard format defined by the authors of LD score regression,

• convert_dataframe_to_markdown_task –

  Prepare results for presentation by converting a dataframe to markdown format.

• copy_file_from_directory_task –

  Copy a file within a DirectoryAsset to create a FileAsset. Useful when downstream tasks require FileAssets.

• copy_task –

  Copy a single file. Mainly used for testing.

• counting_task –

  For testing purposes, recording the number of times that a wrapped task has been executed.

• discard_deps_task_wrapper –

  Save disk space materializing dependencies of the wrapped task in a temporary directory.

• download_file_task –

  Download a file, possibly verifying it using a hash.

• download_files_into_directory_task –

  Task to download one or more files into a directory, then run command line programs on them,

• download_from_google_drive_task –

  Some GWAS summary statistics are stored on Google Drive. Use this task to access them.

• external_directory_copy_task –

  Copies a directory from an external source.

• external_file_copy_task –

  Task to copy a file from an external source. Used to testing.

• extract_all_from_zip_task –

  Task to extract the entire contents of a zip archive

• extract_dataframe_from_rdata_task –
• extract_gzip_task –

  Task to extract a file from a gzip.

• extract_sheet_from_excel_file_task –

  Task to extract sheet from excel file.

• extract_tar_gzip_task –
• extraction_one_file_from_zip_task –
• failing_task –

  A task that always fails, which can be used for testing.

• fake_task –

  A Task that does nothing, which can be used for testing.

• fetch_gget_info_task –

  Task to use gget to annotate gene lists with annotations from genetics databases.

• filter_snps_task –

  Task to filter SNPs in a GWAS according to another table of SNPs passing quality control.

• fixed_effect_meta_analysis_task –

  Task to combine GWAS with fixed-effects meta analysis

• gene_tissue_expression_clustermap_task –

  Task to make a heatmap plot with genes as rows and tissue/cell types as columns

• genetic_correlation_clustermap_task –

  Task to create a heatmap plot illustrating the genetic correlation structure of a collection of traits

• get_file_from_synapse_task –

  Task to get a file from synapse.org, a scientific data repository.

• get_uniprot_reference_data_task –

  Task to download reference data about proteins from UniProt

• gwaslab –

  Tasks using to GWASLab (https://github.com/Cloufield/gwaslab), a Python toolkit for GWAS summary statistics.

• harmonize_gwas_with_reference_table_via_chrom_pos_alleles –

  Given a table of reference genetic variants, harmonize gwas data with that table of reference variants

• harmonize_gwas_with_reference_table_via_rsid –

  Given a table of reference genetic variants, harmonize gwas data with that table of reference variants

• join_dataframes_task –

  Task to perform a SQL-style join.

• lava_task –

  Compute local genetic correlation using LAVA (Local Analysis of [co]Variant Association).

• magma –

  Tasks that are part of the workflow of GWAS-tool MAGMA (Multi-marker Analysis of GenoMic Annotation).

• make_executable_wrapper_task –

  Task to make a file executable by editing unix file permissions (a la chmod).

• mixer –
• multiple_testing_table_task –

  Task to compute a multiple testing correction of a table of p values.

• osf_retrieve_task –

  A task that fetches GWAS data from the Open Science data store

• pipe_dataframe_task –

  Task to transform a dataframe asset using a DataProcessingPipes.

• pipes –

  Pipes are composable DataFrame transformations.

• plot_mr_effect_measure_task –

  Create an effect measure plot using zepid

• r_tasks –

  Tasks that call R libraries.

• specificity_cepo_task –
• specificity_frac_task –
• susie_stacked_plot_task –

  A Task and associated helper methods to plot the results and context of SUSIE fine mapping using stacked panels.

• two_sample_mr_task –

  Task to apply two sample mendelian randomization to GWAS data, together with associated axillary functions.

• upset_plot_task –

  Create an upset plot to describe the intersection of sets represented as dataframe columns

• xr_pipes –

  xr-pipes are composable xarray Dataset transformations.