Function reference

chromake

A snakemake pipeline to align ChIP-seq and ATAC-seq samples.

pipelines.chromake	Chromake pipeline
pipelines.chromake.scripts.config	The config module of chromake contains functions to read and write the config file of the chromake pipeline.
pipelines.chromake.scripts.paths	The paths module of chromake contains functions to identify the inputs and the files generated by the chromake pipeline.
pipelines.chromake.scripts.config.create_example_config	Create an example genomake/chromake YAML configuration file.
pipelines.chromake.scripts.config.update_jobs	Update or add the JOBS section in an existing YAML config.
pipelines.chromake.scripts.config.check_project_and_sequencing	Ensures that projects with no associated sequencing samples are removed from the config, and removes empty sequencing projects, while making sure the mark is considered in the filtering process.
pipelines.chromake.scripts.config.remove_sequencing	Remove an entire sequencing project from the YAML config.
pipelines.chromake.scripts.config.remove_samples	Remove specific samples from a project in the YAML config.
pipelines.chromake.scripts.config.create_samplesheet_from_config	Create a samplesheet table (CSV or Excel) from a YAML config, resolving relative paths
pipelines.chromake.scripts.config.create_config_from_table	Create a YAML config from a table. Supports SAMPLES and optional INPUT files.
pipelines.chromake.scripts.config.check_sample_files_exist	Check if all R1 and R2 FASTQ files listed in the config exist.
pipelines.chromake.scripts.config.check_config_format	Check the configuration file to make sure it follow the requirements of chromake. At runtile, it will stop snakemake if the file format is invalid.
pipelines.chromake.scripts.paths.get_all_sequencings_related_paths	Get the path to the files generated by the pipeline for the samples of all sequencings and projects.
pipelines.chromake.scripts.paths.get_sequencings_related_paths	Get the path to the files generated by the pipeline for the samples of a specific sequencing.
pipelines.chromake.scripts.paths.get_project_paths_for_macs	Get the files necessary for the macs2/macs3 rules of a project.