Snakemake workflow: EMU-smk

This is the Huginn version of the EMU snakemake workflow. Basically, it's just two files, a minimal snakemake file that refers to the one in Github and a configuration file already "configured" to huginn. Please, refer to the public repo for more information.

Usage

1. Preparate the metadata sheet.
2. Run the pipeline
3. Download the RDS file with a phyloseq object ready to analyze.

conda activate snakemake
snakemake --use-conda -n --conda-prefix /software/emu-snakemake
snakemake --use-conda -c50 --conda-prefix /software/emu-snakemake

If you want to keep intermediate output (such as unclassified sequences in a separate fasta or the alignments) use instead:

conda activate snakemake
snakemake --use-conda -n --conda-prefix /software/emu-snakemake --notemp
snakemake --use-conda -c50 --conda-prefix /software/emu-snakemake --notemp