v0.3.2

Bug fixes

• Ignore empty CSV entries when parsing sample information (PR #29).

v0.3.1

Minor updates

• Add --run_information and --demultiplexer arguments to runner workflow (PR #27).

Bug fixes

• Fix detection of sample IDs from Illumina V2 sample sheets (PR #28).

• Provide a clear error message when --run_information is provided but not --demultiplexer (PR #27).

v0.3.0

Major updates

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.

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).

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).

v0.1.0

Initial release