ARPEGGIO v3

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 --lint standards (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 (5.20.1 shown also with badge on Readme)
• Added temporary files in the methylation extraction rules to remove large unused context files and save disk space
• Added --scaffolds option to prevent errors by Bismark when using unfinished genomes (new option added to config file as well)
• Fixed input conditions for DIPLOID_ONLY and POLYPLOID_ONLY modes
• 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

ARPEGGIO Complete

In this new complete version of ARPEGGIO we have:

• Full Conda support, with no need to install anything other than Snakemake
• Full Singularity support, meaning that ARPEGGIO can be run in a container (still using Conda)
• Complete set of analyses with 7 steps: conversion check, quality check, trimming, alignment, deduplication, read sorting, methylation extraction, statistical analyses and downstream analyses on differentially methylated regions
• Different modes supporting 3 experimental designs: polyploid vs diploid parents, polyploid vs polyploid (different conditions) and diploid vs diploid (different conditions)
• Optimal multithreading: ARPEGGIO's rule granularity makes full use of Snakemake's multi-threading option
• A Wiki page provides step-by-step explanations on how to setup and run ARPEGGIO together with some advanced information for more interested users

ARPEGGIO Skeleton

This release includes the first 4 steps of Whole Genome Bisulfite Sequencing data analysis: Quality Control (trimming and quality check), Alignment (Bismark), Read-Sorting (eagle-rc) and Differential Methylation analysis (dmrseq).