workflows/well_demultiplex
Description
Demultiplexing on well level
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 |
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. |
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 Relationships
Used by
1 relationships
Current component
workflows/well_demultiplexhtrnaseq v0.3.0
Uses
1 relationships