https://docs.uabgrid.uab.edu/w/index.php?action=history&feed=atom&title=OneCellPipeOneCellPipe - Revision history2026-04-26T09:56:39ZRevision history for this page on the wikiMediaWiki 1.38.2https://docs.uabgrid.uab.edu/w/index.php?title=OneCellPipe&diff=6001&oldid=prevWwarr@uab.edu: Initial commit2019-12-12T19:31:00Z<p>Initial commit</p>
<p><b>New page</b></p><div>=Summary=<br />
<br />
[https://1cell-bio.com/indrop/#science OneCellPipe] is available for use on Cheaha. From the documentation<ref>https://1cell-bio.com/wp-content/uploads/2019/01/onecellpipe_version-1.1_Dec18.pdf</ref>, OneCellPipe<br />
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<blockquote>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.</blockquote><br />
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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 <code>/tmp</code>. Finally, the pipeline may be run on your data.<br />
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=Setup=<br />
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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 <code>/data/user/<username></code> directory. Replace <code><username></code> with your Cheaha login name. You can use <code>echo $USER</code> to find your login name.<br />
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<pre><br />
cd $USER_DATA<br />
wget https://s3.amazonaws.com/da-ocb-public/onecellpipe.1.19_cf.zip<br />
unzip onecellpipe.1.19_cf.zip<br />
rm onecellpipe.1.19_cf.zip<br />
</pre><br />
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This process should create a subdirectory <code>onecellpipe</code>. Inside that is another directory <code>bin</code>. The file <code>bin/nextflow.singularity.config</code> must be modified. Replace the file contents with the contents of the block below, and save the changes.<br />
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<pre><br />
singularity {<br />
enabled = true<br />
// Adjust this to a shared directory on your system when using compute clusters.<br />
// Also add --cache <DIR> or update the cache variable in bin/nextflow.standard.config when changing this!<br />
cacheDir = '/scratch/<username>'<br />
autoMounts = true<br />
}<br />
</pre><br />
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As mentioned in the comments in the above block, it is also necessary to modify the <code>bin/nextflow.standard.config</code> file. Open that file and find the line starting with <code>cache</code> and replace it with the following.<br />
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<pre><br />
cache = '/scratch/<username>'<br />
</pre><br />
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=Usage=<br />
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To use the pipeline, navigate to the downloaded location of <code>onecellpipe.nf</code> and run the following commands. Replace <code><input_directory></code> with the location of your input files, and replace <code><output_directory></code> with any desired existing subdirectory of <code>/data/user/<username></code>. The <code>--worker $SLURM_NTASKS<code> and <core>--worker2</code> parameters tell the pipeline to use all of the cores available to the SLURM job for parallel processing, which should speed up processing.<br />
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<pre><br />
module load Singularity/2.6.1-GCC-5.4.0-2.26<br />
module load Nextflow/19.10.0<br />
export SINGULARITY_BINDPATH=/data:/<br />
nextflow onecellpipe.nf --dir <input_directory> --out $USER_DATA/<output_directory> --worker $SLURM_NTASKS --worker2 $SLURM_NTASKS<br />
</pre><br />
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=References=<br />
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<references /></div>Wwarr@uab.edu