runner

Description

Runner for demultiplexing of raw sequencing data

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'  
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 v0.5.1 \  
  -main-script target/nextflow/runner/main.nf \  
  -params-file params.yaml

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. The <RunID> is the value passed to the `id` argument.
--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.

Name

Type & Properties

--input

file

required

--run_information

file

--demultiplexer

string

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

Output arguments

Name	Type & Properties	Description
--fastq_output	file output
--sample_qc_output	file output
--multiqc_output	file output
--demultiplexer_logs	file output

Name

Type & Properties

--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.

Name

Type & Properties

--skip_copycomplete_check

boolean_true