API Reference

Main modules

github	GitHub helper functions
jobby	Display job information for past SLURM job IDs.
module_list	module_list
paths
pkg_util	Miscellaneous utility functions for the package
pipeline	Helpers for bioinformatics pipelines
send_email	Send an email with an attachment
shell	Utility functions for shell command execution.
software
spooker	SPOOKER 👻
templates	Template files for CCBR Tools.
versions	Get information from git tags, commit hashes, and GitHub releases.

Pipeline utilities

pipeline.cache	Functions for singularity cache management
pipeline.hpc	Classes for working with different HPC clusters.
pipeline.nextflow	Run Nextflow workflows in local and HPC environments.
pipeline.util	Pipeline utility functions

Legacy tools

GSEA.deg2gs	Reads a rnaseq pipeliner *_DEG_all_genes.txt file and outputs a prioritized list of Ensembl gene IDs for ToppFun
GSEA.multitext2excel	Reads a list of files to import as separate tabs in Excel
GSEA.ncbr_huse	Set of functions supporting the FNL NCBR work
gb2gtf	Module for converting GenBank files to GTF format.
homologfinder.hf	Finds homologs in human and mouse.
intersect	Find the intersect of two files, returns the inner join
jobinfo	Get HPC usage metadata for a list of slurm jobids on biowulf
peek	Take a peek at tab-delimited files