demultiplex/CHANGELOG.md

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).

• Output demultiplexer logs and metrics (PR #41).

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/<run_id>/<date_time_stamp>_demultiplex_<version>/
  

  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/<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