v1.3.0

• allow user to provide custom curation databases
• new metazoa RefSeq 231 database is included for curation (old metazoa database was RefSeq 89)
• NMNH users can submit MitoPilot Hydra jobs directly from the app

Note

To update older MitoPilot projects, please run the R function MitoPilot::backwards_compatibility(). This will add any missing fields to the SQL database and attempt to update the Docker/Singularity container version in your project .config file.

Full Changelog: 1.2.8...1.3.0

v1.2.8

• new curation ruleset for octocorals
• bug fixes for start/stop codon manual editing
• new buttons to manually shift start/stop codon positions in increments of 1, 5, or 10
• "DELETED" message sent to notes instead of warnings field when removing gene annotations
• require sample IDs to only contain alphanumeric characters, dashes, underscores, or colons
• print sample IDs that violate rules when initializing a project
• fixed bug in init_db_userAsmb
• "problematic" field defaults to "no" when initializing a project

Note

To update older MitoPilot projects, please run the R function MitoPilot::backwards_compatibility(). This will add any missing fields to the SQL database and attempt to update the Docker/Singularity container version in your project .config file.

Full Changelog: 1.2.7...1.2.8

v1.2.7

• adds preliminary curation ruleset for copepods
• fixes error in handling of tRNAs with undetermined anticodons
• fixes bug in curation script when correcting overextended negative strand gene start codon positions
• adds warnings filter to Annnotate GUI
• warnings field in the annotate table now reports the total number of warnings rather than the number of genes with warnings
• extra field in annotate table now lists duplicated genes by name rather than a count of total duplicated genes

Important

The extra field in the annotation table will not update unless you rerun the Annotate module.

Note

To update older MitoPilot projects, please run the R function MitoPilot::backwards_compatibility(). This will add any missing fields to the SQL database and attempt to update the Docker/Singularity container version in your project .config file.

Full Changelog: 1.2.6...1.2.7

v1.2.6

• Fixed a start/stop codon bug when MITOS2 annotation wraps around a circular assembly

Full Changelog: 1.2.5...1.2.6

Note

To update older MitoPilot projects, please run the R function MitoPilot::backwards_compatibility(). This will add any missing fields to the SQL database and attempt to update the container version in your project .config file.

v1.2.5

• fixed bug with Nextflow progress output ANSI encoding in the Shiny app

Full Changelog: 1.2.4...1.2.5

Note

To update older MitoPilot projects for this release, please run the R function MitoPilot::backwards_compatibility(). This will add any missing fields to the SQL database. You should also make sure your project's .config file lists the matching container (container = 'macguigand/mitopilot:1.2.5').

v1.2.4

• reject stop codon auto-curation if it introduces an internal stop codon
• fixed bugs with Annotate details stop codon manual editing buttons

Full Changelog: 1.2.3...1.2.4

Note

To update older MitoPilot projects for this release, please run the R function MitoPilot::backwards_compatibility(). This will add any missing fields to the SQL database. You should also make sure your project's .config file lists the matching container (container = 'macguigand/mitopilot:1.2.4').

v1.2.3

Added alternate start codons for NAD1, NAD3, and NAD4L to curation parameters in params_starfish_mito.R based on RefSeq starfish mitogenome annotations.

Full Changelog: 1.2.2...1.2.3

Note

To use old projects with the latest MitoPilot release, please run the function MitoPilot::backwards_compatibility(). This will update the SQL database with any missing fields (columns).

v1.2.2

Changed coverage plotting in the Annotate details panel of the Shiny app.

Full Changelog: 1.2.1...1.2.2

Note

To use old projects with the latest MitoPilot release, please run the function MitoPilot::backwards_compatibility(). This will update the SQL database with any missing fields (columns).

v1.2.1

Fixed the following R functions to work with user-assembly projects

• update_sample_metadata()
• update_sample_seqdata()
• add_samples()
• export_db_to_csv()

Full Changelog: 1.2.0...1.2.1

Note

To use old projects with the latest MitoPilot release, please run the function MitoPilot::backwards_compatibility(). This will update the SQL database with any missing fields (columns).

v1.2.0

What's Changed

• New R function new_project_userAsmb() allows users to create a project with their own mitogenome assemblies

Full Changelog: 1.1.0...1.2.0

Note

To use old projects with the latest MitoPilot release, please run the function MitoPilot::backwards_compatibility(). This will update the SQL database with any missing fields (columns).