https://github.com/oicr-gsi/bcl2fastq
Workflow for Illumina's bcl2fastq
https://github.com/oicr-gsi/bcl2fastq
base-calling bcl2fastq illumina workflow
Last synced: 4 months ago
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Workflow for Illumina's bcl2fastq
- Host: GitHub
- URL: https://github.com/oicr-gsi/bcl2fastq
- Owner: oicr-gsi
- Created: 2015-07-07T19:04:55.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2025-09-10T19:33:51.000Z (11 months ago)
- Last Synced: 2025-09-10T23:35:42.110Z (11 months ago)
- Topics: base-calling, bcl2fastq, illumina, workflow
- Language: C++
- Homepage:
- Size: 4.44 MB
- Stars: 1
- Watchers: 15
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
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README
# bcl2fastq
The workflow wraps around Illumina's bcl2fastq software which demultiplexes sequencing data and converts base call (BCL) files into FASTQ files. For every cycle of a sequencing run, the Real-Time Analysis software generates a BCL file containing base calls and associated quality scores (Q-scores). This is the root workflow as the most NGS applications require FASTQ inputs.
## Overview
## Dependencies
* [bcl2fastq](https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
## Usage
### Cromwell
```
java -jar cromwell.jar run bcl2fastq.wdl --inputs inputs.json
```
### Inputs
#### Required workflow parameters:
Parameter|Value|Description
---|---|---
`lanes`|Array[Int]+|The lane numbers to process from this run
`mismatches`|Int|Number of mismatches to allow in the barcodes (usually, 1)
`modules`|String|The modules to load when running the workflow. This should include bcl2fastq and the helper scripts.
`samples`|Array[Sample]+|The information about the samples. Tname of the sample which will determine the output file prefix. The list of barcodes in the format i7-i5 for this sample. If multiple barcodes are provided, they will be merged into a single output.
`runDirectory`|String|{'description': "The path to the instrument's output directory.", 'vidarr_type': 'directory'}
#### Optional workflow parameters:
Parameter|Value|Default|Description
---|---|---|---
`basesMask`|String?|None|An Illumina bases mask string to use. If absent, the one written by the instrument will be used.
`timeout`|Int|40|The maximum number of hours this workflow can run for.
#### Optional task parameters:
Parameter|Value|Default|Description
---|---|---|---
`process.bcl2fastq`|String|"bcl2fastq"|The name or path of the BCL2FASTQ executable.
`process.bcl2fastqJail`|String|"bcl2fastq-jail"|The name ro path of the BCL2FASTQ wrapper script executable.
`process.extraOptions`|String|""|Any other options that will be passed directly to bcl2fastq.
`process.ignoreMissingBcls`|Boolean|false|Flag passed to bcl2fastq, allows missing bcl files.
`process.ignoreMissingFilter`|Boolean|false|Flag passed to bcl2fastq, allows missing or corrupt filter files.
`process.ignoreMissingPositions`|Boolean|false|Flag passed to bcl2fastq, allows missing or corrupt positions files.
`process.memory`|Int|32|The memory for the BCL2FASTQ process in GB.
`process.temporaryDirectory`|String|"."|A directory where bcl2fastq can dump massive amounts of garbage while running.
`process.threads`|Int|8|The number of processing threads to use when running BCL2FASTQ
### Outputs
Output | Type | Description | Labels
---|---|---|---
`fastqs`|Array[Output]+|A list of FASTQs generated and annotations that should be applied to them.|
## Commands
This section lists command(s) run by bcl2fastq workflow
* Running bcl2fastq
Convert basecalls to fastq
```
BCL2FASTQ_JAIL
-t TMP_DIR
-s SAMPLES_JSON
-- BCL2FASTQ
--barcode-mismatches MISMATCHES
--input-dir INPUT_DIR
--intensities-dir RUN_DIR/Data/Intensities
--no-lane-splitting
--processing-threads THREADS
--runfolder-dir RUN_DIR
--tiles TITLES
--interop-dir TMP_DIR
Optional Parameters:
--ignore-missing-bcls
--ignore-missing-filter
--ignore-missing-positions
--use-bases-mask CUSTOM_BASE_MASK
EXTRA_OPTIONS
```
## Support
For support, please file an issue on the [Github project](https://github.com/oicr-gsi) or send an email to gsi@oicr.on.ca .
_Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)_