The pipeline supports many types of parameters for customization to your compute environment and data. These can all be specified on the command line using the standard syntax --argument="value" or --argument "value". You can also use any option supported by Nextflow itself. Note that certain arguments (i.e. those interpreted by Nextflow) use a single dash instead of two.
You can export variables into your environment before calling the pipeline, or set them on the same line like this:
TMPDIR=/opt/tmp ./examples/stitching.sh
Note that the example scripts set all these directories relative to the TMPDIR by default, so setting TMPDIR sets everything else to the same location.
| Variable | Default | Description |
|---|---|---|
| TMPDIR | /tmp | Directory used for temporary files by certain processes like MATLAB's MCR Cache. |
| SINGULARITY_TMPDIR | /tmp | Directory where Docker images are downlaoded and converted to Singularity Image Format. Needs to be large enough to accomodate several GB, so moving it out of /tmp is sometimes necessary. |
| SPARK_LOCAL_DIR | /tmp | Directory used for temporary storage by Spark (in the stitching module). |
| Argument | Default | Description |
|---|---|---|
| -profile | standard | Configuration profile to use (Valid values: standard, lsf, localdocker) |
| -with-tower | Nextflow Tower URL for monitoring | |
| -work-dir | ./work | Nextflow working directory where all intermediate files are saved |
| --spark_work_dir | Path to directory containing Spark working files and logs during stitching | |
| --runtime_opts | Runtime options for Singularity must include mounts for any directory paths you are using. You can also pass the --nv flag here to make use of NVIDIA GPU resources. For example, --nv -B /your/data/dir -B /your/output/dir |
|
| --lsf_opts | Any extra options to pass to bsub when running jobs on LSF | |
| ‑‑singularity_cache_dir | Path to directory used for caching Singularity container images. If running in distributed mode, this path must be accessible from all cluster nodes. |