broadinstitute/viral-ngs: v1.13.0

New:

• run-pipe.sh now has an option: --wait-submit This prevents immediate submission of all jobs to the cluster scheduler with dependencies, instead letting Snakemake take control of submitting jobs. This is useful because in UGER systems jobs in Eqw count against a user's quota even though Snakemake is unaware of this. The option for --immediate-submit is still the default, but it is overridden if --wait-submit is specified.

Fixed:

• better support for multiple annotations with snpEff
• metagenomics memory requirements have been changed in the Snakemake pipeline to be the total per-job, rather than per-core
• An exception is now raised if inputs cannot be found for the Snakemake rule merge_one_per_sample
• After alignment, reads with leading or trailing indels are remobed prior to V-Phaser2 (previously such reads would cause V-Phaser2 to crash)
• Files with raw reads following the naming convention "sample.bam" can now be used in the assembly report functionality

Changed/Updated:

• snakemake 3.8.2 -> 3.9.0
• Database path in config.yaml for the align_rna metagenomics method has been updated to reflect a newly-built database