Bcl2fastq
Convert bcl files to fastq files using bcl2fastq
Info
ID: bcl2fastq
Namespace: demux
Links
Example commands
You can run the pipeline using nextflow run
.
View help
You can use --help
as a parameter to get an overview of the possible parameters.
nextflow run openpipelines-bio/openpipeline \
-r 1.0.2 -latest \
-main-script target/nextflow/demux/bcl2fastq/main.nf \
--help
Run command
Example of params.yaml
# Arguments
input: # please fill in - example: "bcl_dir"
sample_sheet: # please fill in - example: "SampleSheet.csv"
# output: "$id.$key.output.output"
# reports: "$id.$key.reports.reports"
ignore_missing: false
# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
-r 1.0.2 -latest \
-profile docker \
-main-script target/nextflow/demux/bcl2fastq/main.nf \
-params-file params.yaml
Note
Replace -profile docker
with -profile podman
or -profile singularity
depending on the desired backend.
Argument group
Arguments
Name | Description | Attributes |
---|---|---|
--input |
Input run directory | file , required, example: "bcl_dir" |
--sample_sheet |
Pointer to the sample sheet | file , required, example: "SampleSheet.csv" |
--output |
Output directory containig fastq files | file , required, example: "fastq_dir" |
--reports |
Reports directory | file , example: "reports_dir" |
--ignore_missing |
boolean_true |