workflows/runner

Description

Runner for HT RNA-seq pipeline

Type

nextflow_script

License

MIT

Links

Repository

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
ignore: [ "Undetermined" ]  
umi_length: [ 10 ]  
run_params: "$id.$key.run_params"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \  
  -revision v0.8.3 \  
  -main-script target/nextflow/workflows/runner/main.nf \  
  -params-file params.yaml

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
--run_params	file output

Name

Type & Properties

--input

file

required

--barcodesFasta

file

required

--genomeDir

file

required

--annotation

file

required

--ignore

string

multiple

--umi_length

integer

--run_params

file

output

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

Name

Type & Properties

--id

string

--project_id

string

required

--experiment_id

string

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>/.

Name

Type & Properties

--plain_output

boolean_true

Publish arguments

Name	Type & Properties	Description
--fastq_publish_dir	string required
--results_publish_dir	string required

Name

Type & Properties

--fastq_publish_dir

string

required

--results_publish_dir

string

required