demux/bcl_convert
Description
Convert bcl files to fastq files using bcl-convert.
Information about upgrading from bcl2fastq via
https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html
and https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html
Arguments
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input run directory |
--sample_sheet -s | file required | Pointer to the sample sheet |
--output -o | file required output | Output directory containig fastq files |
--reports | file output | Reports directory |
--test_mode | boolean | Should bcl-convert be run in test mode (using --first-tile-only)? |
--strict_mode | boolean | Abort if any files are missing. |
--tiles | string | Process only a subset of tiles by a regular expression. |
--exclude_tiles | string | Exclude set of tiles by a regular expression |
--no_lane_splitting | boolean | Wheter to avoid splitting FASTQ file by lane. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.fastq_dir"
reports: "$id.$key.reports.reports_dir"
test_mode: [ false ]
strict_mode: [ false ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.2.0 \
-main-script target/nextflow/demux/bcl_convert/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
demux/bcl_convertopenpipeline v4.2.0
Uses
0 relationships
No component dependencies found.