fq/fq_lint
fastq
lint
validate
quality-control
Description
Validates a single or paired FASTQ file.
Input
Name | Type & Properties | Description |
|---|---|---|
--input_1 | file required | Read 1 source. Accepts both raw and gzipped FASTQ inputs. |
--input_2 | file | Read 2 source. Accepts both raw and gzipped FASTQ inputs. |
Options
Name | Type & Properties | Description |
|---|---|---|
--lint_mode | string | Panic on first error or log all errors. |
--single_read_validation_level | string | Only use single read validators up to a given level. |
--paired_read_validation_level | string | Only use paired read validators up to a given level. |
--disable_validator | string multiple | Disable validators by code. Use multiple times to disable more than one. |
--record_definition_separator | string | Define a record definition separator. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
lint_mode: [ "panic" ]
single_read_validation_level: [ "high" ]
paired_read_validation_level: [ "high" ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.0 \
-main-script target/nextflow/fq/fq_lint/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
fq/fq_lintbiobox v0.4.0
Uses
0 relationships
No component dependencies found.