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'  
umi_length: [ 10 ]  
id: "run"  
run_params: "$id.$key.run_params"  
run_metadata: "$id.$key.run_metadata"  
star_output_dir: "$id.$key.star_output_dir"  
nrReadsNrGenesPerChrom_dir: "$id.$key.nrReadsNrGenesPerChrom_dir"  
star_qc_metrics_dir: "$id.$key.star_qc_metrics_dir"  
eset_dir: "$id.$key.eset_dir"  
f_data_dir: "$id.$key.f_data_dir"  
p_data_dir: "$id.$key.p_data_dir"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \  
  -revision v0.14.7 \  
  -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>`. Must contains FASTQ files in the format `PoolName_S_L_R1_001.fastq.gz` where * PoolName is a unique ID for the microwell plates or combination thereof. * S followed by a running number: the sample number based on the order that samples are listed in the sample sheet (that was used to demultiplex the pools) starting with 1 (e.g. S1) * (Optional) the lane number (e.g. L001) * _001 fixed suffix.
--run_id	string	Unique ID for the sequencing run
--barcodesFasta	file required
--genomeDir	file required
--annotation	file required
--pools	string multiple	Filter the FASTQ files in the input directory to only include pools from the provided list. Pool names are inferred from the FASTQ file names (see input argument for more information). By default all pools are included.
--umi_length	integer	Length of the UMI sequences

Name

Type & Properties

--input

file

required

--run_id

string

--barcodesFasta

file

required

--genomeDir

file

required

--annotation

file

required

--pools

string

multiple

--umi_length

integer

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

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

Output arguments

Name	Type & Properties	Description
--run_params	file output
--run_metadata	file output	YAML file containing meta information about the file — .e.g. versions of (sub)-workflows.
--star_output_dir	file output
--nrReadsNrGenesPerChrom_dir	file output
--star_qc_metrics_dir	file output
--eset_dir	file output
--f_data_dir	file output
--p_data_dir	file output

Name

Type & Properties

--run_params

file

output

--run_metadata

file

output

--star_output_dir

file

output

--nrReadsNrGenesPerChrom_dir

file

output

--star_qc_metrics_dir

file

output

--eset_dir

file

output

--f_data_dir

file

output

--p_data_dir

file

output