Releases: COMBINE-lab/simpleaf
v0.17.2
Install simpleaf 0.17.2
Install prebuilt binaries via shell script
curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/simpleaf/releases/download/v0.17.2/simpleaf-installer.sh | shDownload simpleaf 0.17.2
| File | Platform | Checksum |
|---|---|---|
| simpleaf-aarch64-apple-darwin.tar.xz | Apple Silicon macOS | checksum |
| simpleaf-x86_64-apple-darwin.tar.xz | Intel macOS | checksum |
| simpleaf-x86_64-unknown-linux-gnu.tar.xz | x64 Linux | checksum |
v0.17.1
Install simpleaf 0.17.1
Install prebuilt binaries via shell script
curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/simpleaf/releases/download/v0.17.1/simpleaf-installer.sh | shDownload simpleaf 0.17.1
| File | Platform | Checksum |
|---|---|---|
| simpleaf-aarch64-apple-darwin.tar.xz | Apple Silicon macOS | checksum |
| simpleaf-x86_64-apple-darwin.tar.xz | Intel macOS | checksum |
| simpleaf-x86_64-unknown-linux-gnu.tar.xz | x64 Linux | checksum |
v0.17.0
v0.16.2
v0.16.1
v0.16.0
0.16.0 (2024-01-29)
This release makes relatively few surface level changes, but represents a minor (rather than patch) version bump because it sets piscem as the default index and mapper, and paves the way to remove the --use-piscem flag in the future. In the current release, the --use-piscem flag is still accepted, but it is the default behavior, and need not be explicitly provided. Additionally, a --no-piscem flag has been added to the index and quant commands, and the --no-piscem flag is necessary to use the alevin-fry associated flags and options to those commands.
The plan in future release (likely from 0.17 forward) will be to remove the --use-piscem flag entirely, and just keep the --no-piscem flag, as this will simplify argument parsing and also remove redundant flags.
This flag also fixed a bug with the parsing of , separated lists to the --decoy-paths flag, and fixed a few typos in error messages.
Features
- make piscem default, add --no-piscem flag (1642732)
Bug Fixes
v0.15.1
v0.15.0
0.15.0 (2023-10-24)
This release adds a major new feature to simpleaf, the ability to patch workflows (either workflow templates, or fully-instantiated manifests). Detailed documentation about the patch sub-command of the workflow command is provided in the corresponding documentation page. However, at a high-level, the main idea is that patching lets one take a workflow template, where many of the relevant fields have been filled out by the user, and then programatically generate many manifests where specific fields are parameterized by an input parameter table. In simpler terms, provides the ability to use a sample table to automatically generate many workflow manifests, one per sample, that can then be executed by simpleaf.
However, the patching mechanism is both more flexible and general than the ability to simply provide a sample table, as any valid fields in the workflow can be overridden, and since patches are applied before instantiation of the workflow template into a manifest, it is even possible to patch top-level variables that affect many parts of the configuration. Yet, we imagine that "sample sheet" functionality will be the most common use-case for the patch sub-command, and so that capability should be relatively easy and straightforward to use. We encourage users to try out this feature and please provide feedback and suggestions to improve the user experience!
In addition to this major new feature, this release also incorporates several small but important changes detailed below.
Support for advanced indexing and mapping options exposed in piscem >= 0.7
Piscem 0.7 introduces a new option during indexing, and several new (optional) parameters during mapping. These are now exposed in the latest version of simpleaf. Note, these parameters do not make sense if you are not using piscem for mapping, or if your version of piscem is < 0.7. Thus, simpleaf will issue an error if you attempt to use the new piscem indexing flag with an older version of piscem. Likewise, during mapping, simpleaf will issue a warning and drop the new mapping parameters if you are using an older version of piscem (however, if intended these warnings can be safely ignored, they simply designate that the new flags will not be applied to the mapping process).
Updates to protocol estuary workflows
As our understanding of the capabilities and common idioms in the powerful jsonnet languages has evloved, so to has the structure of the workflows we have developed in the protocol estuary. It is therefore essential that, when updating to this new version of simpleaf, you refresh your local copy of the protocol estuary by issuing the simpleaf workflow refresh command.
The updated templates have been written to be cleaner, to avoid redundancy where possible, and critically, to support the key new feature of patching templates and manifests. In addition to a rewrite of the workflow templates, some changes have been made to the system varaiable names assumed in templates by simpleaf.
Updates to reserved names in templates
The following "system variables" (i.e. important variable names assumed by simpleaf when parsing and processing workflows) have changed.
Arguments=>argumentsActive=>activeStep=>stepProgram Name=>program_name
Updates to common fields in protocol estuary templates
Additionally, while not required for the structure of user-developed workflows, or directly part of the system variables assumed by simpleaf, the main components of the protocol estuary templates have been changed as indicated below. In general, for unifiormity, we recommend these as relevant section names in user-developed workflows.
Recommended Configuration=>fast_configOptional Configuration=>advanced_config
Features
-
support for workflow template and manifest patching.
-
advanced params for piscem >= 0.7 (a19b492)