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Run pipeline

Learn about how it is easy to launch pipeline in all the ways users want.

The design of how to launch the pipeline reflects our philosophy about pipeline and the effort to realize superb user experience.

Dry-run

Set --dryrun flag to examine how many scheduled tasks to be performed before actually executing the pipeline. Here one task could be aligning one FASTQ file, or counting UMI from one SAM alignment file.

celseq2 --config-file /path/to/wonderful_CEL-Seq2_config.yaml \
    --experiment-table /path/to/wonderful_experiment_table.txt \
    --output-dir /path/to/result_dir \
    --dryrun

Launch pipeline to run parallel tasks

Set -j 10 to launch pipeline with 10 tasks executed in parallel. This can run on either the computing node or your own computer.

celseq2 --config-file /path/to/wonderful_CEL-Seq2_config.yaml \
    --experiment-table /path/to/wonderful_experiment_table.txt \
    --output-dir /path/to/result_dir \
    -j 10

Submit tasks to server

Alternatively, it is straightforward to run the pipeline of celseq2 by submitting jobs to cluster, as celseq2 is built on top of snakemake which is a powerful workflow management framework.

For example, user could run the following command to submit jobs to computing nodes. Here it submits 10 jobs in parallel with 50G of memory requested by each.

celseq2 --config-file /path/to/wonderful_CEL-Seq2_config.yaml \
    --experiment-table /path/to/wonderful_experiment_table.txt \
    --output-dir /path/to/result_dir \
    -j 10 \
    --cluster "qsub -cwd -j y -l h_vmem=50G" &