workflows/well_demultiplex

Description

Demultiplexing on well level

Type

nextflow_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output_r1: "$id.$key.output_r1._*"  
output_r2: "$id.$key.output_r2._*"  
pool: "$id.$key.pool"  
well_id: "$id.$key.well_id"  
barcode: "$id.$key.barcode"  
lane: "$id.$key.lane"  
pair_end: "$id.$key.pair_end"  
n_wells: .nan  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/workflows/well_demultiplex/main.nf \  
  -params-file params.yaml

Input arguments

Name	Type & Properties	Description
--input_r1	file required multiple	Forward reads in FASTQ format. Multiple files can be provided which will be demultiplexed separately before joining the results for each individual well.
--input_r2	file required multiple	Reverse reads in FASTQ format. Multiple files can be provided which will be demultiplexed separately before joining the results for each individual well.
--barcodesFasta	file required

Name

Type & Properties

--input_r1

file

required

multiple

--input_r2

file

required

multiple

--barcodesFasta

file

required

Output arguments

Name	Type & Properties	Description
--output_r1	file required multiple output	List of demultiplexed fastq files
--output_r2	file required multiple output	List of demultiplexed fastq files
--pool	string output	The original pool / sample name
--well_id	string output
--barcode	string output
--lane	string output
--pair_end	string output
--n_wells	integer output	The number of wells in the pool is well is a part of.

Name

Type & Properties

--output_r1

file

required

multiple

output

--output_r2

file

required

multiple

output

--pool

string

output

--well_id

string

output

--barcode

string

output

--lane

string

output

--pair_end

string

output

--n_wells

integer

output