About

Renne Lab

Principal Investigator: Rolf Renne
Henry E. Innes Professor of Cancer Research
University of Florida
UF Health Cancer Center
UF Department of Molecular Genetics and Microbiology
UF Genetics Institute
http://www.RenneLab.com

Lead Developer

Dan Stribling <ds@ufl.edu>
https://github.com/dstrib
https://orcid.org/0000-0002-0649-9506
University of Florida, Renne Lab

Changelog

v0.11-dev - ongoing:

  • Refinements

  • Bugfixes

  • Added additional template nextflow.config files for task

  • Added macOS support for Conda machines (for all dependencies)

  • Added input data file integrity checks to Merge process

  • Added internal output checks for early error catching

  • Updated Conda Bowtie2 Version to 2.4.4 and added component dependency

  • Merge “validate” and “validate-all” modes into “validate” mode

  • Remove “dry-run” mode as low utility per complexity

  • Switch to nextflow-implementation of memory handling

  • Add support for task execution via Docker / Singularity containers

  • Corrected error in handling of normalized alignment files

  • Moved SEACR to external dependency config

  • Removed CUTRUNTools:kseqtest from pipeline

  • Migrate aumotated testing from TravisCI to CircleCI

  • Add Beta support for Singularity/Docker dependency configurations

  • Add CircleCI Docker dependency config testing

  • Add default Singularity and Docker support configs via profiles

v0.10 - 2020-09-04:

  • Refinements

  • Changed verbose task logging to implementation with “beforeScript”

  • Complete Initial Documentation

  • Moved macs2 peak-calling out of alpha testing

  • “Reordered” output step directories

  • Tuned resource usage defaults

  • Added process memory usage categories

  • Move UCSC/Kent tools to external dependency setup

  • Added bigWig track format creation step

  • Overhauled alignment modification step

  • Removed Picard dependency

  • Changed (non-track) alignment output files to CRAM (compressed BAM)

v0.09:

  • Refinements

  • Added one-step database preparation

  • Implemented ‘list_refs’ mode

  • Implemented automatic reference paramater finding

  • Shifted paramaters to config files

  • Implemented initiate mode

  • Added minimal documentation

  • Added UCSC (faCount) automated installation

  • Added automated acquisition of Trimmomatic adapters

  • Implemented MACS2 peak calling

  • Added autodetection of tag sequence length

v0.08:

  • Initial Github Upload