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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 enables using only the lane 2 for analysis. To opt in a tile set, first exclude all tiles, then include tiles.

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.

Add a Missing Flow Cell ID (--flowcell-id)

The following example overwrites the default flow cell ID from RunParameters.json.

docker run --rm -v </path/to/input>:/input -v </path/to/output>:/output bases2fastq /input /output -p 8 --flowcell-id 123abc123

Use a Corrected Run Manifest (-r)

The following cases require a corrected run manifest:

  • You sequenced indexed libraries with a run manifest that does not include index sequences.
  • During sequencing, you did not upload a run manifest with indexed samples. Use a corrected run manifest with all samples and their associated index sequences to demultiplex.
  • A Bases2Fastq execution failed or reported incorrect results due to incorrect settings or indexes in the run manifest, requiring reprocessing.

See the Run Manifest Documentation for run manifest preparation instructions.

docker run --rm -v </path/to/input>:/input -v </path/to/output>:/output bases2fastq /input /output -p 8 -r /input/<corrected_manifest_filename.csv>

QC-Only Mode (--qc-only)

The following example executes in QC-only mode on 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.

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 Run Manifest Settings.

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"