# demultiplex v0.4.0 ## Breaking changes * Falco has been replaced with FastQC. Falco generates FastQC compatible output, but fails to run on empty FASTQ files (PR #51). - `runner` workflow: `falco_output` has been renamed to `output_sample_qc`. - `demultiplex` workflow: `output_falco` has been renamed to `output_sample_qc`. - The output file names from the sample QC no longer contains the input file extensions. Instead, the sample name is used. (for example `sample1_S1_R2_001.fastq.gz_fastqc_report.html` becomes `sample1_S1_R2_001_fastqc_report.html`) * `demultiplex` workflow: `output_multiqc` argument has been renamed to `multiqc_output` in order to align inner workflow and runner (PR #51). # demultiplex v0.3.12 ## New features * Add support for Nextflow versions version starting 25.xx.xx (PR #50). ## Bug fixes * Allow FASTQ files for `Undetermined` to be empty (PR #50). # demultiplex v0.3.11 ## New features * Output demultiplexer logs and metrics (PR #41). # demultiplex v0.3.10 ## Minor changes * Moved the test resources to their new location (PR #37). # demultiplex v0.3.9 ## Bug fixes * Fix defaults for output arguments in nextflow schema's. * Fix an issue where an integer being passed to a argument with `type: double` resulted in an error (PR #44). ## Minor changes * Bump viash to 0.9.4, which adds support for nextflow versions starting major version 25.01 (PR #43 and #44). # demultiplex v0.3.8 ## Bug fixes * Provide a proper error when a FASTQ file is empty after demultiplexing (PR #40). # demultiplex v0.3.7 ## Minor updates * Ignore lines starting with '#' when parsing run information CSV (PR #39). # demultiplex v0.3.6 ## Minor updates * Allow letter case variants for headers when looking for sample information in run information CSV (PR #38). # demultiplex v0.3.5 ## Breaking changes * The `demultiplex` workflow now outputs a list of directories for the `output_falco` argument (one for each barcode) instead of one directory for the complete run. The output from the `runner` workflow remained unchanged (PR #33). ## Minor updates * In case Illumina data is detected in the input folder, check for the presence of the 'copyComplete.txt' file. This check can be disabled using `--skip_copycomplete_check` (PR #34). # demultiplex v0.3.4 ## Minor updates * Resource labels are now automatically included during build (PR #32). # demultiplex v0.3.3 ## Breaking change - The `runner` defines the output differently now: - The last part of the `--input` path is expected to be the run ID and this run ID is used to create the output directory. - If the input is `file.tar.gz` instead of a directory, the `file` part is used as the run ID. - The output structure is then as follows: ``` $publish_dir//_demultiplex_/ ``` For instance: ``` $publish_dir └── 200624_A00834_0183_BHMTFYDRXX └── 20241217_051404_demultiplex_v1.2 ├── run_information.csv ├── fastq │   ├── Sample1_S1_L001_R1_001.fastq.gz │   ├── Sample23_S3_L001_R1_001.fastq.gz │   ├── SampleA_S2_L001_R1_001.fastq.gz │   ├── Undetermined_S0_L001_R1_001.fastq.gz │   └── sampletest_S4_L001_R1_001.fastq.gz └── qc ├── fastqc │   ├── Sample1_S1_L001_R1_001.fastq.gz_fastqc_data.txt │   ├── Sample1_S1_L001_R1_001.fastq.gz_fastqc_report.html │   ├── Sample1_S1_L001_R1_001.fastq.gz_summary.txt │   ├── Sample23_S3_L001_R1_001.fastq.gz_fastqc_data.txt │   ├── Sample23_S3_L001_R1_001.fastq.gz_fastqc_report.html │   ├── Sample23_S3_L001_R1_001.fastq.gz_summary.txt │   ├── SampleA_S2_L001_R1_001.fastq.gz_fastqc_data.txt │   ├── SampleA_S2_L001_R1_001.fastq.gz_fastqc_report.html │   ├── SampleA_S2_L001_R1_001.fastq.gz_summary.txt │   ├── Undetermined_S0_L001_R1_001.fastq.gz_fastqc_data.txt │   ├── Undetermined_S0_L001_R1_001.fastq.gz_fastqc_report.html │   ├── Undetermined_S0_L001_R1_001.fastq.gz_summary.txt │   ├── sampletest_S4_L001_R1_001.fastq.gz_fastqc_data.txt │   ├── sampletest_S4_L001_R1_001.fastq.gz_fastqc_report.html │   └── sampletest_S4_L001_R1_001.fastq.gz_summary.txt └── multiqc_report.html ``` - This logic can be avoided by providing the flag `--plain_output`. # Minor updates * Added `output_run_information` argument that copies the run information file to the output (PR #31). # demultiplex v0.3.2 # Bug fixes * Ignore empty CSV entries when parsing sample information (PR #29). # demultiplex 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). # demultiplex 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 `$publish_dir/`. The workflow has two optional flags to be used in combination with `--id`: - `--add_date_time`: rather than publishing the results under `$publish_dir`, this adds an additional layer `$publish_dir//`. This is useful when you want to keep track of multiple runs of the workflow (example: `240322_143020`). - `--add_workflow_id`: adding this flag will add `_demultiplex_` to the output directory (example: `demultiplex_v0.2.0`). When starting the workflow from a non-release, the version will be set to `version_unkonwn`. The default structure in the output directory is: - Two sub-directories: - `fastq` - `qc` for the reports: - `multiqc_report.html` - `fastqc/` directory containing the different fastqc (falco) reports. The `$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