Workflow to produce FASTQ files from an Illumina instrument's run directory
java -jar cromwell.jar run bcl2fastq.wdl --inputs inputs.json
| 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'} |
| 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. |
| 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 |
| Output | Type | Description |
|---|---|---|
fastqs |
Array[Output]+ | A list of FASTQs generated and annotations that should be applied to them. |
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
For support, please file an issue on the Github project or send an email to [email protected] .
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