# demultiplex x.y.z

## Major updates
The outflow of the workflow has been refactored to be more flexible. This is done by creating a wrapper workflow `runner` that wraps the native `demultiplex` workflow. The `runner` workflow is responsible for setting the output directory based on the input arguments:

3 arguments exist for specifying the relative location of the 3 _outputs_ of the workflow:

- `fastq_output`: The directory where the demultiplexed fastq files are stored.
- `falco_output`: the directory for the `fastqc`/`falco` reports.
- `multiqc_output`: The filename for the `multiqc` report.

The target location path is determined by the following logic:

- If no `id` is provided, the output directory is set to `$publish_dir`.
- If an `id` is explicitly set using Seqera Cloud or by adding `--id <>`, the output directory is set to `$publish_dir/<id>`.

The workflow has two optional flags to be used in combination with `--id`:

- `--add_date_time`: rather than publishing the results under `$publish_dir`, this adds an additional layer `$publish_dir/<date-time-stamp>/`. This is useful when you want to keep track of multiple runs of the workflow (example: `240322_143020`).
- `--add_workflow_id`: adding this flag will add `_demultiplex_<version>` to the output directory (example: `demultiplex_v0.2.0`). When starting the workflow from a non-release, the version will be set to `version_unkonwn`.

The default structure in the output directory is:

- Two sub-directories:
  - `fastq`
  - `qc` for the reports:
    - `multiqc_report.html`
    - `fastqc/` directory containing the different fastqc (falco) reports.

The `$publish_dir` variable corresponds to the argument provided with `--publish-dir`. The `date-time-stamp` is generated by the workflow based on when it was launched and is thus guaranteed to be unique.

# demultiplex v0.2.0

## Breaking changes

* `demultiplex` workflow: renamed `sample_sheet` argument to `run_information` (PR #24)

## New features

* Add support for `bases2fastq` demultiplexer (PR #24)

## Minor updates

* Add resource labels to workflows (PR #21).

# demultiplex v0.1.1

## Minor updates

* Bump viash to 0.9.0 (PR #14).

* `demultiplex` workflow: use `v0.2.0` release instead of `main` branch for `biobox` dependencies (PR #11).

* Renamed `biobase` repository to `biobox` (PR #13 and PR #15).

# demultiplex v0.1.0

Initial release