runner
Description
Runner for demultiplexing of raw sequencing data
Input arguments
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Base directory of the canonical form `s3://<bucket>/<path>/<RunID>/`. A tarball (tar.gz, .tgz, .tar) containing run information can be provided in which case the RunID is set to the name of the tarball without the extension. |
--run_information | file | CSV file containing sample information, which will be used as input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina) or 'RunManifest.csv' (Element Biosciences). If not specified, will try to autodetect the sample sheet in the input directory. Requires --demultiplexer to be set. |
--demultiplexer | string | Demultiplexer to use, choice depends on the provider of the instrument that was used to generate the data. When not using --sample_sheet, specifying this argument is not required. |
Annotation flags
Name | Type & Properties | Description |
|---|---|---|
--plain_output | boolean_true | Flag to indicate that the output should be stored directly under $publish_dir rather than under a subdirectory structure runID/<date_time>_demultiplex_<version>/. |
Output arguments
Name | Type & Properties | Description |
|---|---|---|
--fastq_output | file output | |
--sample_qc_output | file output | |
--multiqc_output | file output | |
--demultiplexer_logs | file output |
Other arguments
Name | Type & Properties | Description |
|---|---|---|
--skip_copycomplete_check | boolean_true | Disable the check for the presence of a "CopyComplete.txt" file in input directory in case of Illumina data. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
fastq_output: "$id.$key.fastq_output"
sample_qc_output: "$id.$key.sample_qc_output"
multiqc_output: "$id.$key.multiqc_output"
demultiplexer_logs: "$id.$key.demultiplexer_logs"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/demultiplex.git \
-revision v0.4.4 \
-main-script target/nextflow/runner/main.nf \
-params-file params.yaml Relationships
Used by
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No components use this component.
Current component
runnerdemultiplex v0.4.4
Uses
2 relationships