The outflow of the workflow has been refactored to be more flexible (PR #19). 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.
