Skip to contents

Update old project database for backwards compatibility

Source: R/backwards_compatibility.R
backwards_compatibility.Rd

Migrates an old project's SQLite database to the current schema and refreshes the curation rules. Each migration step is guarded by an existence check, so the function is idempotent and safe to re-run; already-current projects report "nothing to update" and exit without changes. Migrations include, among others:

  • annotate: "reviewed", "ID_verified", "problematic", "partial", "orf_opts" columns.

  • annotate_opts: "start_gene", ARWEN / Aragorn / MitoFinder / tRNAscan / MITOS toggles and options, coverage/feature trimming, and reference db columns.

  • assemble_opts: "assembler", "mitofinder_db"/"mitofinder", "max_paths", "max_scaffolds", "min_assembly_length", "join_scaffolds".

  • curate_opts: "max_blast_hits", "ref_dir", "ref_db", "linear_complete" (and rewriting the legacy in-container Mitos2 ref path to the GitHub-hosted reference db).

  • assemble: "poor_blast_ref" (migrated from samples and normalized to TEXT), BLAST result columns, "blast_opts".

  • samples: numeric "genetic_code" (rebuilding any legacy TEXT column as INTEGER so assembly does not crash).

  • New tables: "orf_opts", "blast_opts", "export_opts", "scaffold_mappings", "assemblies", "assembly_blast", and the "blast_ref_annotations"/"blast_ref_sequences"/"blast_ref_alignment" set.

Usage

backwards_compatibility(path = ".", executor = NULL, update_config = TRUE)

Arguments

path

Path to the project directory (default = current working directory)

executor

The executor whose config template to regenerate from. Same options as [new_project()]: a built-in template ("local", "awsbatch", "slurm", "sge", "pbs", "lsf", "NMNH_Hydra", "NOAA_SEDNA") or the name of a saved cluster profile (see [list_configs()]). Required when `update_config = TRUE`.

update_config

Regenerate the Nextflow `.config` from the `executor` template (default `TRUE`). Set to `FALSE` to migrate only the SQLite database and leave the existing `.config` untouched.

Details

When `update_config = TRUE` the Nextflow `.config` is regenerated wholesale from the template for the supplied `executor` (rather than patched line by line): the project-specific values (raw/asmb dirs, min depth, genetic code, NCBI key, and, for generic HPC templates, queue / penv / clusterOptions / container engine) are carried over, the container is bumped to the current MitoPilot version, and the previous `.config` is saved to a timestamped `.config.bak.<timestamp>` backup. Because an existing config may carry hand edits that cannot be parsed reliably (e.g. a multi-line `clusterOptions` closure), the executor must be given explicitly and you should review the regenerated config against the backup.