New version of ARPEGGIO formatted following the new code standards available via the snakemake --lint command. In addition all the tools have been updated to their latest versio and minor fixes have been implemented. For details see the log below:
Updates in ARPEGGIO v3:
Major
- Code adapted to follow
snakemake --lintstandards (https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html?highlight=lint#best-practices) - New GitHub action to format code with
snakefmt(https://github.com/snakemake/snakefmt) - Added rule in Snakefile to check config file for mistakes in the conditional parameters
- ARPEGGIO is now tested with GitHub Actions and not with TravisCI anymore
Minor
- Added minimum Snakemake version requirement (
5.20.1shown also with badge on Readme) - Added temporary files in the methylation extraction rules to remove large unused context files and save disk space
- Added
--scaffoldsoption to prevent errors by Bismark when using unfinished genomes (new option added to config file as well) - Fixed input conditions for
DIPLOID_ONLYandPOLYPLOID_ONLYmodes - Updated tools' versions:
trim-galore=0.6.5 -> 0.6.6
fastqc=0.11.8 -> 0.11.9
bismark=0.22.3 -> 0.23.0
samtools=1.10 -> 1.11
multiqc=1.8 -> 1.9
bioconductor-dmrseq=1.6.0 -> 1.10.0
r-base=3.6.2 -> 4.0.3
r-data.table=1.12.8 -> 1.13.6
bedtools=2.29.1 -> 2.29.2
r-stringi=1.4.3 -> 1.5.3