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| 1 | +# UniverSC |
| 2 | + |
| 3 | +## Single-cell processing across technologies |
| 4 | + |
| 5 | +UniverSC is an open-source single-cell pipeline that runs across platforms on various technologies. |
| 6 | + |
| 7 | +## Maintainers |
| 8 | + |
| 9 | +Tom Kelly (RIKEN, IMS) |
| 10 | + |
| 11 | +Kai Battenberg (RIKEN CSRS/IMS) |
| 12 | + |
| 13 | +Contact: <first name>.<family name>[at]riken.jp |
| 14 | + |
| 15 | +## Implementation |
| 16 | + |
| 17 | +This container runs Cell Ranger v3.0.2 installed from source on MIT License on GitHub with |
| 18 | +modifications for compatibility with updated dependencies. All software is installed from |
| 19 | +open-source repositories and available for reuse. |
| 20 | + |
| 21 | +It is _not_ subject to the 10X Genomics End User License Agreement (EULA). |
| 22 | +This version allows running Cell Ranger v3.0.2 on data generated from any experimental platform |
| 23 | +without restrictions. However, updating to newer versions on Cell Ranger subject to the |
| 24 | +10X EULA is not possible without the agreement of 10X Genomics. |
| 25 | + |
| 26 | +To comply with licensing and respect 10X Genomics Trademarks, the 10X Genomics logo |
| 27 | +has been removed from HTML reports, the tool has been renamed, and proprietary |
| 28 | +closed-source tools to build Cloupe files are disabled. |
| 29 | + |
| 30 | +It is still suffient to generate summary reports and count matrices compatible with |
| 31 | +single-cell analysis tools available for 10X Genomics and Cell Ranger output format |
| 32 | +in Python and R packages. |
| 33 | + |
| 34 | +## Usage |
| 35 | + |
| 36 | +### Generating References |
| 37 | + |
| 38 | +The Cell Ranger modules can be used to generate reference indexes to run UniverSC. |
| 39 | +Note that UniverSC requires the Open Source version v3.0.2 of Cell Ranger included |
| 40 | +in the nf-core/universc Docker image. The same module parameters can be run provided |
| 41 | +that the container is changed in process configurations (modify nextflow.config). |
| 42 | + |
| 43 | +``` |
| 44 | +process { |
| 45 | +
|
| 46 | +... |
| 47 | + withName: CELLRANGER_MKGTF { |
| 48 | + container = "nfcore/universc:1.2.5.1" |
| 49 | + } |
| 50 | + withName: CELLRANGER_MKREF{ |
| 51 | + container = "nfcore/universc:1.2.5.1" |
| 52 | + } |
| 53 | +... |
| 54 | +} |
| 55 | +``` |
| 56 | + |
| 57 | +This will generate a compatible index for UniverSC using the same version of the |
| 58 | +STAR aligner and a permissive software license without and EULA. |
| 59 | + |
| 60 | +### Container settings |
| 61 | + |
| 62 | +The cellranger install directory must have write permissions to run UniverSC. |
| 63 | +To run in docker or podman use the `--user root` option in container parameters |
| 64 | +and for singularity use the `--writeable` parameter. |
| 65 | + |
| 66 | +These are set as default in universc/main.nf: |
| 67 | + |
| 68 | +``` |
| 69 | + container "nfcore/universc:1.2.5.1" |
| 70 | + if (workflow.containerEngine == 'docker'){ |
| 71 | + containerOptions = "--privileged" |
| 72 | + } |
| 73 | + if (workflow.containerEngine == 'podman'){ |
| 74 | + containerOptions = "--runtime /usr/bin/crun --userns=keep-id --user root --systemd=always" |
| 75 | + } |
| 76 | + if (workflow.containerEngine == 'singularity'){ |
| 77 | + containerOptions = "--writable" |
| 78 | + } |
| 79 | +``` |
| 80 | + |
| 81 | +Select the container engine with `nextflow --profile "docker"` or set the environment variable |
| 82 | +as one of the following before running nextflow. |
| 83 | + |
| 84 | +``` |
| 85 | +export PROFILE="docker" |
| 86 | +export PROFILE="podman" |
| 87 | +export PROFILE="singularity" |
| 88 | +``` |
| 89 | + |
| 90 | +Note that due to dependencies installed in a docker image, it is not possible to use conda environments. |
| 91 | + |
| 92 | +## Disclaimer |
| 93 | + |
| 94 | +We are third party developers not affiliated with 10X Genomics or any other vendor of |
| 95 | +single-cell technologies. We are releasing this code on an open-source license which calls Cell Ranger |
| 96 | +as an external dependency. |
| 97 | + |
| 98 | +## Licensing |
| 99 | + |
| 100 | +This package is provided open-source on a GPL-3 license. This means that you are free to use and |
| 101 | +modify this code provided that they also contain this license. |
| 102 | + |
| 103 | +## Updating the package |
| 104 | + |
| 105 | +The tomkellygenetics/universc:<VERSION> container is automatically updated with tomkellygenetics/universc:latest. |
| 106 | + |
| 107 | +A stable release is mirrored at nfcore/universc:1.2.5.1 and will be updated as needed. |
| 108 | + |
| 109 | +To build an updated container use the Dockerfile provided here: |
| 110 | + |
| 111 | +[https://github.com/minoda-lab/universc/blob/master/Dockerfile](https://github.com/minoda-lab/universc/blob/master/Dockerfile) |
| 112 | + |
| 113 | +Note that this uses a custom base image which is built with an open-source implementation of |
| 114 | +Cell Ranger v3.0.2 on MIT License and relies of Python 2. The build file can be found here: |
| 115 | + |
| 116 | +[https://github.com/TomKellyGenetics/cellranger_clean/blob/master/Dockerfile](https://github.com/TomKellyGenetics/cellranger_clean/blob/master/Dockerfile) |
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