workflows/runner
Description
Runner for HT RNA-seq pipeline
Input arguments
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>` |
--barcodesFasta | file required | |
--genomeDir | file required | |
--annotation | file required | |
--ignore | string multiple | Pool names to ignore. |
--umi_length | integer | Length of the UMI sequences |
Metadata arguments
Name | Type & Properties | Description |
|---|---|---|
--id | string | Unique identifier for the run |
--project_id | string required | Project ID |
--experiment_id | string required | Experiment ID |
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>/. |
Publish arguments
Name | Type & Properties | Description |
|---|---|---|
--fastq_publish_dir | string required | |
--results_publish_dir | string required |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
ignore: [ "Undetermined" ]
umi_length: [ 10 ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \
-revision v0.7.2 \
-main-script target/nextflow/workflows/runner/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
workflows/runnerhtrnaseq v0.7.2