Release 0.8.0

[farchaab]

PR for version 0.8.0

Summary

Big release with multiple bug fixes and new features:

Changes

command line

• Added snaketool for easy-to-use command line
• Added rich-click for beautiful command line
• Added commands for genome download, read simulation and hmp templates generation
• Added test command to test genome download and read simulation
• Added example scheduler profiles for SLURM

input

• Renamed input table headers (see examples)
• Support path to local fastas as input for read simulation

community design

• Use bases instead of reads for calculating sequencing coverage per genome
• Support reads, bases, sequence and taxonomic abundances for calculating genome abundances
• Multiple samples with different genomes can be simulated in a single run
• Added optional replicate generation
• Added example hmp communities Standard input tables for human samples #5

genome download

• assembly_finder now uses ncbi-datasets-cli for fast genome downloads
• No more NCBI key or email required to download (but recommended)

fasta processing

• Added rule for renaming fastas (avoid names that make snakemake bug)
• Added rule for extracting fastas with sequence id in header (short sequence names for BAM files)
• Added rule for splitting fastas into contigs
• Added rule for calculating genome stats (size, contig number...) when no assembly summary table is provided

read simulation

• Updated long read simulation (pbsim3) to support ONT r10.4.1 and PacBio hifi read generation
• Parallel read compression, shuffling and anonymizing
• Output optional indexed and sorted BAM files
• Output optional biobox taxonomic profile
• Support custom error profiles for art_illumina

Github workflows

• Built documentation on metagenlab.github.io/MeSS/
• Unit tests with minimal data

Fixes

#14
#13