v1.6.0 bactopia/bactopia "Harpoon" - 2021/01/22 Added bactopia pull to pre-build Singularity images --singularity_cache parameter to set location of image downloads --registry to choose Docker registry to use (DockerHub, GitHub, Quay) --max_downloads sets maximum number of downloads (FASTQ/assembly) allowed at once --min_time sets the minimum amount of time a job should be given bactopia search now uses POST requests, and groups accessions into single query strip HTML from FASTA headers used in BLAST Dockerfiles now have conda.md5 label to determine if rebuild is necessary MD5 is updated in Dockerfile when env is updated AMRFinder+ database is now provided by bactopia datasets Parameterized profile (slurm, awsbatch, etc...) variables bactopia build will retry in case of HTTP connection issues --include_tool will build Bactopia Tool environments GitHub Actions build Docker containers on new release (or manual trigger) test that the Conda environment yamls are still valid test bactopia with conda on Linux and OSX test bactopia on Linux with Docker and Singularity Fixed redundant environment version files failed FASTQ/Assembly downloads no longer stop whole run --max_retry is honored now antimicrobial_resistance process honors amrdir variable change directory antimicrobial_resistance to antimicrobial-resistance rename check_staging.py to check-staging.py for consistency Bactopia not producing valid exit code on failure Removed --containerPath variable is replaced by --singularity_cache Native Singularity recipes, will now convert Docker to Singularity docs are now on bactopia.github.io repo