ctmrbio/stag-mwc: StaG v0.6.1

This StaG release is a maintenance release, fixing some things that did not work fully as intended in the previous release, most specifically making sure that the KrakenUniq module works as intended, also when bypassing quality control and host removal steps. It's been approximately one and a half month since the last StaG release (v0.6.1 was released 2023-04-17) and this release contains 23 commits and affects 17 files in the repo. A total of 120 lines were added and 67 removed.

The most notable changes are:

• BBMap: now outputs sorted BAM file, added options keep_sam and keep_bam.
• Bowtie2: added option keep_bam.

• KrakenUniq: environment variable LC_ALL has been added to Singularity image to prevent unnecessary warning messages related to it being undefined.
• KrakenUniq: now able to run when host removal is skipped, solved by adding krakenuniq_merge_reads rule to create a temporary merged fasta file with input data for KrakenUniq to avoid giving KrakenUniq symlinks as input.

• MetaPhlAn: Updated to v4.0.6
• HUMAnN3: Updated to v3.7
• HUMAnN3: Changed the way the temporary directory is resolved, now using Snakemake's built-in resources.tmpdir. This should prevent HUMAnN from creating large temporary directories outside of Slurm job folders so that they cannot be automatically cleaned up if the Slurm job times out or fails before HUMAnN can clean up after itself.
• KrakenUniq: Concatenate reads with BBMap's fuse.sh with a padding of one N instead of interleaving the paired inputs into a single FASTA to avoid KrakenUniq treating paired reads independently.

• Kaiju, Kraken2, MetaPhlAn: area plot removed due to repeatedly leading to failed runs in cached Singularity containers. The script still works as intended in newer matplotlib versions and will remain in the scripts folder for potential manual use if desired.

• Groot: Removed settings related to read length window as that feature was removed in a previous StaG release.