CI
214329783f
Build pipeline: viash-hub.demultiplex.main-zst7j
Source commit: 0d4c4584f0
Source message: Only publish transfer_complete.txt file when the exit code is 0 (#58)
243 lines
8.4 KiB
Markdown
243 lines
8.4 KiB
Markdown
# demultiplex v0.4.4
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## Bug fixes
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* Only add the `transfer_complete.txt` files when the exitcode for the workflow is 0 (PR #58)
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# demultiplex v0.4.3
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## Minor changes
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* The `runner` creates a `transfer_completed.txt` file when the publishing of the output has finished (PR #57).
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# demultiplex v0.4.2
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## Minor changes
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* Provide output from `runner` workflow so it can be used as part of a larger workflow (PR #56).
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* Add workflow identifier to version information during pipeline run (PR #56).
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# demultiplex v0.4.1
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## Minor changes
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* Split off part of the workflow logic (`detect_demultiplexer`) from the main workflow to a dedicated subworkflow (PR #52).
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* Add the package config (`_viash.yaml`) to every component's target dir. This makes introspection from, e.g. a `runner` workflow much more robust (PR #53).
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# demultiplex v0.4.0
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## Breaking changes
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* Falco has been replaced with FastQC. Falco generates FastQC compatible output, but fails to run on empty FASTQ files (PR #51).
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- `runner` workflow: `falco_output` has been renamed to `output_sample_qc`.
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- `demultiplex` workflow: `output_falco` has been renamed to `output_sample_qc`.
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- The output file names from the sample QC no longer contains the input file extensions. Instead, the sample name is used.
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(for example `sample1_S1_R2_001.fastq.gz_fastqc_report.html` becomes `sample1_S1_R2_001_fastqc_report.html`)
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* `demultiplex` workflow: `output_multiqc` argument has been renamed to `multiqc_output` in order to align inner workflow and runner (PR #51).
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# demultiplex v0.3.12
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## New features
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* Add support for Nextflow versions version starting 25.xx.xx (PR #50).
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## Bug fixes
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* Allow FASTQ files for `Undetermined` to be empty (PR #50).
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# demultiplex v0.3.11
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## New features
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* Output demultiplexer logs and metrics (PR #41).
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# demultiplex v0.3.10
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## Minor changes
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* Moved the test resources to their new location (PR #37).
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# demultiplex v0.3.9
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## Bug fixes
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* Fix defaults for output arguments in nextflow schema's.
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* Fix an issue where an integer being passed to a argument with `type: double` resulted in an error (PR #44).
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## Minor changes
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* Bump viash to 0.9.4, which adds support for nextflow versions starting major version 25.01 (PR #43 and #44).
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# demultiplex v0.3.8
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## Bug fixes
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* Provide a proper error when a FASTQ file is empty after demultiplexing (PR #40).
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# demultiplex v0.3.7
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## Minor updates
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* Ignore lines starting with '#' when parsing run information CSV (PR #39).
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# demultiplex v0.3.6
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## Minor updates
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* Allow letter case variants for headers when looking for sample information in run information CSV (PR #38).
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# demultiplex v0.3.5
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## Breaking changes
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* The `demultiplex` workflow now outputs a list of directories
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for the `output_falco` argument (one for each barcode) instead of one directory
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for the complete run. The output from the `runner` workflow remained
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unchanged (PR #33).
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## Minor updates
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* In case Illumina data is detected in the input folder, check for the presence of the 'copyComplete.txt' file.
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This check can be disabled using `--skip_copycomplete_check` (PR #34).
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# demultiplex v0.3.4
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## Minor updates
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* Resource labels are now automatically included during build (PR #32).
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# demultiplex v0.3.3
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## Breaking change
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- The `runner` defines the output differently now:
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- 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.
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- If the input is `file.tar.gz` instead of a directory, the `file` part is used as the run ID.
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- The output structure is then as follows:
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```
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$publish_dir/<run_id>/<date_time_stamp>_demultiplex_<version>/
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```
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For instance:
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```
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$publish_dir
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└── 200624_A00834_0183_BHMTFYDRXX
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└── 20241217_051404_demultiplex_v1.2
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├── run_information.csv
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├── fastq
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│ ├── Sample1_S1_L001_R1_001.fastq.gz
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│ ├── Sample23_S3_L001_R1_001.fastq.gz
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│ ├── SampleA_S2_L001_R1_001.fastq.gz
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│ ├── Undetermined_S0_L001_R1_001.fastq.gz
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│ └── sampletest_S4_L001_R1_001.fastq.gz
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└── qc
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├── fastqc
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│ ├── Sample1_S1_L001_R1_001.fastq.gz_fastqc_data.txt
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│ ├── Sample1_S1_L001_R1_001.fastq.gz_fastqc_report.html
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│ ├── Sample1_S1_L001_R1_001.fastq.gz_summary.txt
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│ ├── Sample23_S3_L001_R1_001.fastq.gz_fastqc_data.txt
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│ ├── Sample23_S3_L001_R1_001.fastq.gz_fastqc_report.html
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│ ├── Sample23_S3_L001_R1_001.fastq.gz_summary.txt
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│ ├── SampleA_S2_L001_R1_001.fastq.gz_fastqc_data.txt
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│ ├── SampleA_S2_L001_R1_001.fastq.gz_fastqc_report.html
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│ ├── SampleA_S2_L001_R1_001.fastq.gz_summary.txt
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│ ├── Undetermined_S0_L001_R1_001.fastq.gz_fastqc_data.txt
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│ ├── Undetermined_S0_L001_R1_001.fastq.gz_fastqc_report.html
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│ ├── Undetermined_S0_L001_R1_001.fastq.gz_summary.txt
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│ ├── sampletest_S4_L001_R1_001.fastq.gz_fastqc_data.txt
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│ ├── sampletest_S4_L001_R1_001.fastq.gz_fastqc_report.html
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│ └── sampletest_S4_L001_R1_001.fastq.gz_summary.txt
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└── multiqc_report.html
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```
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- This logic can be avoided by providing the flag `--plain_output`.
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# Minor updates
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* Added `output_run_information` argument that copies the run information file to the output (PR #31).
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# demultiplex v0.3.2
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# Bug fixes
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* Ignore empty CSV entries when parsing sample information (PR #29).
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# demultiplex v0.3.1
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# Minor updates
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* Add `--run_information` and `--demultiplexer` arguments to `runner` workflow (PR #27).
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# Bug fixes
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* Fix detection of sample IDs from Illumina V2 sample sheets (PR #28).
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* Provide a clear error message when `--run_information` is provided but not `--demultiplexer` (PR #27).
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# demultiplex v0.3.0
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## Major updates
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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:
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3 arguments exist for specifying the relative location of the 3 _outputs_ of the workflow:
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- `fastq_output`: The directory where the demultiplexed fastq files are stored.
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- `falco_output`: the directory for the `fastqc`/`falco` reports.
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- `multiqc_output`: The filename for the `multiqc` report.
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The target location path is determined by the following logic:
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- If no `id` is provided, the output directory is set to `$publish_dir`.
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- If an `id` is explicitly set using Seqera Cloud or by adding `--id <>`, the output directory is set to `$publish_dir/<id>`.
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The workflow has two optional flags to be used in combination with `--id`:
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- `--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`).
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- `--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`.
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The default structure in the output directory is:
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- Two sub-directories:
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- `fastq`
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- `qc` for the reports:
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- `multiqc_report.html`
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- `fastqc/` directory containing the different fastqc (falco) reports.
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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.
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# demultiplex v0.2.0
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## Breaking changes
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* `demultiplex` workflow: renamed `sample_sheet` argument to `run_information` (PR #24)
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## New features
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* Add support for `bases2fastq` demultiplexer (PR #24)
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## Minor updates
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* Add resource labels to workflows (PR #21).
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# demultiplex v0.1.1
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## Minor updates
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* Bump viash to 0.9.0 (PR #14).
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* `demultiplex` workflow: use `v0.2.0` release instead of `main` branch for `biobox` dependencies (PR #11).
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* Renamed `biobase` repository to `biobox` (PR #13 and PR #15).
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# demultiplex v0.1.0
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Initial release
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