To run this Snakemake pipeline, you need to generate a config yaml file:
shortname: tolid
workingdirectory: directory in which the markerscan results are stored
outdir: directory in which to store the final output files, e.g. /lustre/scratch124/tol/projects/darwin/data/insects/$scientific_name/assembly/draft/
stsfile: /lustre/scratch123/tol/tolqc/track/tol_sts.tsv
scientific_name: full scientific name, e.g. Tromatobia_lineatoria
gfafile: location of the gfa file (needs to correspond with the assembly which markerscan used)
pwd_directory: directory in which to store temporary files generated by this pipeline
taxfile: location of the tax file from MarkerScan (*SSU.reduced.SILVA.tax)
email: email address from where to send emails to ENA taxid requests, if you leave this as an empty string emails will not be sent
You now can run this using Singularity:
singularity pull docker://emvcaest/wolbachia_submission:latest
singularity run wolbachia_submission.sif snakemake --cores $threads --use-conda --conda-prefix /opt/conda/ -s /WolbachiaSubmission/Snakefile --configfile $configfile