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Changelog

Source: NEWS.md

metaboWorkflows 0.10.2

  • hrmtargets::tar_export() is now used in project templates to track exported files.

  • The generated Rmarkdown reports now include the project name in the file name.

  • The argument parallel_plan has been added to defineProject() to allow the specification of the future parallel plan in the generated project.

metaboWorkflows 0.10.1

  • Clarified the specification of argument type in the documentation of target().

  • Added a suitable pre-treatment target expression for processing GC-MS profiling data.

metaboWorkflows 0.10.0

  • Workflow templates now include a _targets.yaml file for targets configuraion settings.

  • Workflow templates now include a customised .Rprofile file.

  • Target factories from packages other than targets or tarchetypes can now be specified in targets().

  • The Dockerfile is now generated with the latest tag if the hrm-docker release information cannot be accessed with a warning printed if so.

  • The template grover input targets now correctly track the .mzML files without causing an error if the mzML target later becomes invalidated. grover::runInfo() is now used to retrieve the sample information.

  • The targets option garbage_collection is now set as TRUE in targets::tar_option_set() in the template R/utils.R to improve memory usage during pipeline execution.

metaboWorkflows 0.9.6

  • Ensure that the latest hrm-docker tag date is selected for the output project template Dockerfile.

metaboWorkflows 0.9.5

  • The correct sample information table is now exported for the pre-treated data.

metaboWorkflows 0.9.4

  • Plotting and summary targets added to the spectral processing module for profiling workflows.

  • Script edited header added to generated R/utils.R file.

  • Added the prettycode package to suggests.

metaboWorkflows 0.9.3

  • The workflow parallel options now set in R/utils.R.

  • The targets "transient" memory option now set for all targets in tar_options_set() in R/utils.R.

  • Updated the package introduction vignette to include the setting of package options in R/utils.R.

metaboWorkflows 0.9.2

  • Renamed relevant targets with the prefixes results and parameters.

  • R Markdown output report chunks now also include targets with the prefixes results and parameters.

  • Captions for summary tables in R Markdown report output are generated from the target name.

  • Modelling feature importance target now replaced by a modelling explanatory features target.

  • Fixed typo in R Markdown report output footer.

  • Project scripts generated by projecttemplates and then edited by metaboWorkflows now include a header comment denoting the version of the package used.

  • Targets for workflow modules now written to individual scripts within the project R/targets directory. These scripts are then sourced by _targets.R.

  • Updated the usage vignettes with relevant changes.

metaboWorkflows 0.9.1

  • Added titles to supervised and unsupervised random forest MDS plots.

  • rawrr package now install now directed to Bioconductor for renv initialisation.

metaboWorkflows 0.9.0

  • Added a NEWS.md file to track changes to the package.

  • A package website is now available at https://jasenfinch.github.io/metaboWorkflows/.

  • The package can now be used to firstly define a workflow and then generate a project template directory that facilitates reproducible analysis powered by the use of targets package, renv, git and docker.

  • A choice of workflow data inputs are now available that include file paths and converted data file retrieval from a grover web API.

  • Workflows can be defined using defineWorkflow() based the workflow input type and metabolomic technique, also enabling the selection of project template parameters.

  • Workflow definitions can be modified which is detailed in the Workflow customisation and extension vignette.

  • Project directories for workflow definitions can be generated using generateWorkflow().

  • The Introduction vignette has been updated to detail the new package functionality.