Example Execution Commands
The following examples show optional arguments in Bases2Fastq execution commands. The examples use general template commands with local storage.
Adjust Tiles (--include-tile, --exclude-tile)
The following example uses the --exclude-tile and --include-tile optional arguments to only include lane 2 in the Bases2Fastq execution. To include a tile set, you must first exclude all tiles, then include the desired tiles.
- Docker
- Static Binary
docker run --rm -v </path/to/input>:/input -v </path/to/output>:/output bases2fastq /input /output -p 8 --exclude-tile "L.*R..C..S." --include-tiles L2R..C..S.
./bases2fastq input output -p 8 --exclude-tile L*R..C..S. --include-tiles L2R..C..S.
Add a Missing Flow Cell ID (--flowcell-id)
The following example overwrites the default flow cell ID from RunParameters.json.
- Docker
- Static Binary
docker run --rm -v </path/to/input>:/input -v </path/to/output>:/output bases2fastq /input /output -p 8 --flowcell-id 123abc123
./bases2fastq input output -p 8 --flowcell-id 123abc123
Use a Corrected Run Manifest (-r)
The following example replaces an original run manifest with a corrected version. For information on corrected run manifests, see the Run Manifest Documentation.
- Docker
- Static Binary
docker run --rm -v </path/to/input>:/input -v </path/to/output>:/output bases2fastq /input /output -p 8 -r /input/<corrected_manifest_filename.csv>
./bases2fastq input output -p 8 -r /path/to/corrected_manifest_filename.csv
QC-Only Mode (--qc-only)
- Docker
- Static Binary
The following example executes in QC-only mode for one tile.
docker run --rm -v </path/to/input>:/input -v </path/to/output>:/output bases2fastq /input /output -p 8 --qc-only
The following example executes in QC-only mode for all tiles in lane 1:
docker run --rm -v </path/to/input>:/input -v </path/to/output>:/output bases2fastq /input /output -p 8 --qc-only --include-tiles L1R..C..S.
The following example executes in QC-only mode for a single tile.
./bases2fastq input output -p 8 --qc-only
The following example executes in QC-only mode for all tiles in Lane 1:
./bases2fastq input output -p 8 --qc-only --include-tiles L1R..C..S.
Adjust Run Manifest Settings (--settings)
Settings in the run manifest can be overwritten in the Bases2Fastq execution command. For a complete list of settings, see the Run Manifest Documentation.
- Docker
- Static Binary
The following example generates a FASTQ file for Index 1 and a UMI FASTQ file.
docker run --rm -v </path/to/input>:/input -v </path/to/output>:/output bases2fastq /input /output -p 8 --settings "I1Fastq,True" --settings "UmiFastQ,True"
The following example enables single-end adapter trimming for Read 2.
docker run --rm -v </path/to/input>:/input -v </path/to/output>:/output bases2fastq /input /output -p 8 --settings "R2AdapterTrim,True" --settings "AdapterTrimType,Single-End"
The following example generates a FASTQ file for Index 1 and a UMI FASTQ file.
./bases2fastq input output -p 8 --settings "I1Fastq,True" --settings "UmiFastQ,True"
The following example enables single-end adapter trimming for Read 2.
./bases2fastq input output -p 8 --settings "R2AdapterTrim,True" --settings "AdapterTrimType,Single-End"