update metadata and docs

CHANGES.md

+2024-11-14
+
+Initial version.
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LICENSE.md

+Copyright © 2023. The University of Texas Southwestern Medical Center
+5323 Harry Hines Boulevard Dallas, Texas, 75390 Telephone 214-648-3111
+
+CELLxGENE license:
+
+The MIT License (MIT)
+
+Copyright (c) 2017-2023 Chan Zuckerberg Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
\ No newline at end of file

README.md

-# scRNA_analysis_pipeline
+# Single cell RNA analysis pipeline
 
+This Astrocyte workflow chains four Strand lab scRNA analysis workflows together
+into a pipeline. This pipeline performs the following steps:
 
+1. Alignment and counting with cellranger-count
+2. Ambient RNA cleanup with cellbender
+3. Filtering and pre-processing following Strand lab guidelines
+4. Interactive visualization with CZ CELLxGENE
 
-## Getting started
-
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
-
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://git.biohpc.swmed.edu/astrocyte/workflows/strand-lab/scrna_analysis_pipeline.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://git.biohpc.swmed.edu/astrocyte/workflows/strand-lab/scrna_analysis_pipeline/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+This pipeline is currently under development. Stay tuned!
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astrocyte_pkg.yml

+#
+# metadata for the cellranger-count workflow package
+#
+
+# -----------------------------------------------------------------------------
+# BASIC INFORMATION
+# -----------------------------------------------------------------------------
+
+# A unique identifier for the workflow package, text/underscores only
+name: 'scRNA_analysis_pipeline'
+# Who wrote this?
+author: 'John Lafin'
+# A contact email address for questions
+email: 'john.lafin@utsouthwestern.edu'
+# A more informative title for the workflow package
+title: 'scRNA analysis pipeline'
+# A summary of the workflow package in plain text
+description: |
+  This is a workflow for a full, boilerplate analysis of single cell/nucleus
+  RNAseq data. This workflow accepts FASTQ files as input, and will perform
+  alignment, counting, ambient RNA correction, filtering, and pre-processing,
+  then produce an interactive session for exploration in a VizApp.
+
+#### New Features in Astrocyte 0.4.0 and above ####
+citation: |
+  Nextflow 23.04.3: https://www.nextflow.io/
+  10x Genomics Cell Ranger: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
+  CellBender: https://doi.org/10.1038/s41592-023-01943-7
+  R: https://www.R-project.org/
+  CZ CELLxGENE: https://doi.org/10.1101/2021.04.05.438318
+
+  R packages used:
+  Seurat, version 5.1.0
+  scDblFinder, version 1.16.0
+  dplyr, version 1.1.4
+  ggplot2, version 3.5.1
+  future, version 1.34.0
+
+  Please acknowledge support in publications:
+  This research was supported in part by the computational resources provided
+  by the BioHPC supercomputing facility located in the Lyda Hill Department of
+  Bioinformatics, UT Southwestern Medical Center, TX.
+
+# The minimum Astrocyte version that requires to run this workflow. For old pipelines, which do not have this label
+# a default value of 0.3.1 will be assigned automatically. A request of minimum version less than 0.4.0 will be ignored.
+minimum_astrocyte_version: '2.0.0'
+# The Nextflow version that requires to run this workflow.  For old pipelines, which do not have this label
+# a default value of 0.31.0 will be assigned automatically. Please make sure the requested nextflow version is available
+# in the module list.
+nextflow_version: '23.04.3'
+# (Optional) The Nextflow config file to use for this workflow. If provided, the file should exist in workflow/configs
+nextflow_config: 'biohpc.config'
+# The container to use for this workflow, none/singularity. If omitted, the default value 'none' will be used.
+container: 'singularity'
+singularity_version: '3.9.9'
+
+# -----------------------------------------------------------------------------
+# DOCUMENTATION
+# -----------------------------------------------------------------------------
+
+# A list of documentation file in .md format that should be viewable from the
+# web interface. These files are in the 'docs' subdirectory. The first file
+# listed will be used as a documentation index and is index.md by convention
+# To supply a title for documentation use a pair of [ 'filename', 'title' ]
+
+documentation_files:
+  - [ 'index.md', 'Help' ]
+
+# -----------------------------------------------------------------------------
+# NEXTFLOW WORKFLOW CONFIGURATION
+# -----------------------------------------------------------------------------
+
+# Remember - The workflow file is always named 'workflow/main.nf'
+#            The workflow must publish all final output into $baseDir
+
+# A list of cluster environment modules that this workflow requires to run.
+# Specify versioned module names to ensure reproducibility.
+workflow_modules:
+  - 'singularity/3.9.9'
+
+# A list of container images requires to run this workflow.
+# Specify full path and version names to ensure reproducibility.
+# This keyword is required when 'container' is specified in Astrocyte 0.4.1 and above.
+# Singularity supports different registries, please specify the protocol to use.
+# Such as, "docker://", "shub://", "library://", etc. We encourage you to use the GitLab
+# container registry of BioHPC to save and manage your container images.
+workflow_containers:
+  - docker://quay.io/nf-core/cellranger:8.0.0
+  - docker://us.gcr.io/broad-dsde-methods/cellbender:0.3.0
+  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/strand-lab/scrna-qc/scrna-qc:1.0.0
+  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/strand-lab/cellxgene/h5ad_convert:0.0.1
+
+# A list of parameters used by the workflow, defining how to present them,
+# options etc in the web interface. For each parameter:
+#
+# REQUIRED INFORMATION
+#  id:         The name of the parameter in the NEXTFLOW workflow
+#  type:       The type of the parameter, one of:
+#                string      - A free-format string
+#                integer     - An integer
+#                real        - A real number
+#                file        - A single file from user data
+#                files       - One or more files from user data
+#                select      - A selection from a list of values
+#                multiselect - One or more selections from a list of values
+#  required:    true/false, must the parameter be entered/chosen?
+#  description: A user friendly description of the meaning of the parameter
+#
+# OPTIONAL INFORMATION
+#  default:   A default value for the parameter (optional)
+#  min:       Minium value/characters/files for number/string/files types
+#  max:       Maximum value/characters/files for number/string/files types
+#  regex:     A regular expression that describes valid entries / filenames
+#
+# SELECT TYPE
+#  choices:   A set of choices presented to the user for the parameter.
+#             Each choice is a pair of value and description, e.g.
+#
+#             choices:
+#               - [ 'myval', 'The first option']
+#               - [ 'myval', 'The second option']
+#
+# NOTE - All parameters are passed to NEXTFLOW as strings... but they
+#        are validated by astrocyte using the information provided above
+
+workflow_parameters:
+
+  - id: sample_sheet
+    type: file
+    required: true
+    regex: ".*csv$"
+    description: |
+      A sample sheet in CSV format. See documentation below for required formatting.
+
+  - id: fastq
+    type: files
+    required: true
+    regex: ".*(fastq|fq).gz"
+    description: |
+      The fastq.gz files to be passed to cellranger count, typically generated
+      by cellranger mkfastq or bcl2fastq.

docs/index.md

+# Single cell RNA analysis pipeline
+
+This Astrocyte workflow chains four Strand lab scRNA analysis workflows together
+into a pipeline. This pipeline performs the following steps:
+
+1. Alignment and counting with cellranger-count
+2. Ambient RNA cleanup with cellbender
+3. Filtering and pre-processing following Strand lab guidelines
+4. Interactive visualization with CZ CELLxGENE
+
+This pipeline is currently under development. Stay tuned!
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