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