Releases: CCBR/CHARLIE
Releases · CCBR/CHARLIE
CHARLIE 0.11.1
- CHARLIE was falsely throwing a file permissions error for tempdir values containing bash variables. (#118, @kelly-sovacool)
- Singularity bind paths were not being set properly. (#119, @kelly-sovacool)
- Update docker containers to set
$PYTHONPATH
. (#119, #125, @kelly-sovacool)- Otherwise, this environment variable can be carried over and cause package conflicts when singularity is not run with
-C
. - Also use
python -E
to ensure the$PYTHONPATH
is not carried over. (#129, @kelly-sovacool)
- Otherwise, this environment variable can be carried over and cause package conflicts when singularity is not run with
- Fix
reconfig
to correctly replace variables in the config file. (#121, @kelly-sovacool) - Prevent using excessive memory when copying reference files. (#126, @kelly-sovacool)
- Fix missing output files due to file system latency and use real (absolute) paths where possible. (#130, @kelly-sovacool)
- Update documentation to reflect biowulf usage and improved test dataset. (#132, @kelly-sovacool)
CHARLIE 0.11.0
- Major updates to convert CHARLIE from a biowulf-specific to a platform-agnostic pipeline (#102, @kelly-sovacool):
- All rules now use containers instead of envmodules.
- Default config and cluster config files are provided for use on biowulf and FRCE.
- New entry
TEMPDIR
in the config file sets the temporary directory location for rules that require transient storage. - New
--singcache
argument to provide a singularity cache dir location. The singularity cache dir is automatically set inside/data/$USER/
or$WORKDIR/
if--singcache
is not provided.
- Minor documentation improvements. (#114, @kelly-sovacool)
v0.10.1
v0.9.0
Significant upgrades since the last release:
- updates to wrapper script, many new arguments/options added
- new
per-sample
counts table format - new
all-sample
master counts matrix withmin-nreads
filtering andntools
column to show number of tools supporting the circRNA call - new version of Snakemake
cluster_status
script added for forced completion of pipeline upon TIMEOUTs- updated flowchart from lucid charts
- added circRNAfinder, find_circ, circExplorer2_bwa and other tools
- optimized execution and resource requirements
- updated viral annotations (Thanks Sara!)
- new method to extract linear counts, create linear BAMs using circExplorer2 outputs
- new job reporting using
jobby
and its derivatives - separated creation of BWA and BOWTIE2 index from creation of STAR index to speed things up
- parallelized
find_circ
- better cleanup (eg. deleting _STARgenome folders, etc.) for much smaller digital footprint
- multitude of comments throughout the snakefiles including listing of output file column descriptions
- preliminary GH actions added