OneCellPipe

=Summary=

OneCellPipe is available for use on Cheaha. From the documentation, OneCellPipe

"is a software wrapper ... which controls the management and execution of the indrops software pipeline for processing single-cell sequencing data generated using 1CellBio’s inDrop™ sequencing technology. The software leverages the NextFlow workflow management software to control the processing steps in a validated and consistent Singularity environment."

As mentioned, the pipeline is available as a NextFlow pipeline file which automatically downloads dependencies. To make this work seamlessly with Cheaha, some setup and modifications need to be done. The first step is to obtain the pipeline. The second step is to modify the Singularity configuration so cache files do not use. Finally, the pipeline may be run on your data.

=Setup=

To obtain the pipeline, use the following commands in a terminal in an interactive job. They will download the pipeline from a public repository and place it in the  directory. Replace  with your Cheaha login name. You can use  to find your login name.

cd $USER_DATA wget https://s3.amazonaws.com/da-ocb-public/onecellpipe.1.19_cf.zip unzip onecellpipe.1.19_cf.zip rm onecellpipe.1.19_cf.zip

This process should create a subdirectory. Inside that is another directory. The file  must be modified. Replace the file contents with the contents of the block below, and save the changes.

singularity { enabled = true // Adjust this to a shared directory on your system when using compute clusters. // Also add --cache  or update the cache variable in bin/nextflow.standard.config when changing this! cacheDir = '/scratch/ ' autoMounts = true }

As mentioned in the comments in the above block, it is also necessary to modify the  file. Open that file and find the line starting with  and replace it with the following.

cache = '/scratch/ '

=Usage=

To use the pipeline, navigate to the downloaded location of  and run the following commands. Replace  with the location of your input files, and replace   with any desired existing subdirectory of. The  parameters tell the pipeline to use all of the cores available to the SLURM job for parallel processing, which should speed up processing.

module load Singularity/2.6.1-GCC-5.4.0-2.26 module load Nextflow/19.10.0 export SINGULARITY_BINDPATH=/data:/ nextflow onecellpipe.nf --dir  --out $USER_DATA/ --worker $SLURM_NTASKS --worker2 $SLURM_NTASKS

=References=