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Q([r,t,o]).pipe(l(([{height:i},{offset:s,size:a},{x:c,y:f}])=>({offset:{x:s.x-c,y:s.y-f+i},size:a})))}(()=>{function e(n,o){parent.postMessage(n,o||"*")}function t(...n){return n.reduce((o,i)=>o.then(()=>new Promise(s=>{let a=document.createElement("script");a.src=i,a.onload=s,document.body.appendChild(a)})),Promise.resolve())}var r=class extends EventTarget{constructor(n){super(),this.url=n,this.m=i=>{i.source===this.w&&(this.dispatchEvent(new MessageEvent("message",{data:i.data})),this.onmessage&&this.onmessage(i))},this.e=(i,s,a,c,f)=>{if(s===`${this.url}`){let u=new ErrorEvent("error",{message:i,filename:s,lineno:a,colno:c,error:f});this.dispatchEvent(u),this.onerror&&this.onerror(u)}};let o=document.createElement("iframe");o.hidden=!0,document.body.appendChild(this.iframe=o),this.w.document.open(),this.w.document.write(`

Changelog

CRUISE development version

New features

  • Trim adapters with cutadapt.
  • Run mageck count. (#9)
  • mageck count only runs if a count table isn't given.
  • Optional: run mageck test and mle. (#9)
  • mageck mle only runs if a design matrix is given.
  • Optional: run drugZ. (#10)
  • Optional: run BAGEL2. (#11)
  • fc (fold change)
  • bf (bayes factor)
  • pr (precision recall)
  • CLI (#16)
  • cruise init to initialize a project directory.
  • cruise run
    • --mode slurm to submit a slurm job to biowulf or frce.
    • --main path/to/main.nf to select a different local install of cruise, or specify the repo (CCBR/CRUISE) to get it from GitHub.

Last update: 2023-10-16
\ No newline at end of file diff --git a/contributing/index.html b/contributing/index.html new file mode 100644 index 0000000..4025564 --- /dev/null +++ b/contributing/index.html @@ -0,0 +1,5 @@ + How to contribute - CRUISE

Contributing to CRUISE

TODO -- describe gitflow, require PRs...

Use pre-commit hooks

Pre-commit can automatically format your code, check for spelling errors, etc. every time you commit.

Install pre-commit if you haven't already, then run pre-commit install to install the hooks specified in .pre-commit-config.yaml. Pre-commit will run the hooks every time you commit.

Versions

Increment the version number following semantic versioning1 in the VERSION file.

Changelog

Keep the changelog up to date with all notable changes in CHANGELOG.md2.

VS code extensions

If you use VS code, installing nf-core extension pack is recommended.

Installation

For testing and debugging, We recommend installing the dev version of cruise to a user-specific location.

git clone https://github.com/CCBR/CRUISE
+mkdir -p ~/bin/cruise
+pip install ./CRUISE -t ~/bin/cruise
+export PATH="$HOME/bin/cruise/bin:$PATH"
+

  1. semantic versioning guidelines https://semver.org/ 

  2. changelog guidelines: https://keepachangelog.com/en/1.1.0/ 


Last update: 2023-10-16
\ No newline at end of file diff --git a/getting-started/index.html b/getting-started/index.html new file mode 100644 index 0000000..1556964 --- /dev/null +++ b/getting-started/index.html @@ -0,0 +1,8 @@ + Getting Started with CRUISE - CRUISE

Getting Started with CRUISE

TODO intro paragraph

Installation

CRUISE is installed on the Biowulf and FRCE clusters as part of the ccbrpipeliner module. If you'd like to run the pipeline in a different execution environment, take a look at how to run the nextflow pipeline directly.

Prepare a sample sheet

TODO

Initialize

Copy the configuration files to your current working directory

cruise init
+

Run

TODO preview, stub, mode=slurm

TODO required params

Run preview to view processes that will run:

cruise run -profile test -preview
+

Launch a stub run to view processes that will run and download containers:

cruise run -profile test,singularity -stub
+

Run the test dataset using the test profile:

cruise run -profile test,singularity
+

or explicitly specify the output directory and input:

cruise run -profile singularity --outdir results/test --input assets/samplesheet_test.csv
+

Custom reference genome

TODO different required params

Create and use a custom reference genome:

cruise run -profile test -entry MAKE_REFERENCE
+cruise run -profile test -c results/test/genome/custom_genome.config
+

Last update: 2023-10-16
\ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..e228eee --- /dev/null +++ b/index.html @@ -0,0 +1,15 @@ + CRUISE

CRUISE 🛳️

**C**rispr sc**R**een seq**U**encIng analy**S**is pip**E**line

🚧 This project is under active development. It is not yet ready for production use. 🚧

build

Set up

Cruise is installed on the Biowulf HPC. For installation in other execution environments, refer to the docs.

Biowulf

Cruise is available on Biowulf in the ccbrpipeliner module. You'll first need to start an interactive session and create a directory from where you'll run cruise.

# start an interactive node
+sinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200
+# make a working directory for your project and go to it
+mkdir -p /data/$USER/chipseq
+cd /data/$USER/chipseq
+# load the ccbrpipeliener module
+module load ccbrpipeliner
+

Usage

Initialize and run cruise with test data:

# copy the cruise config files to your current directory
+cruise init
+# preview the cruise jobs that will run with the test dataset
+cruise run --mode local -profile test -preview
+# launch a cruise run on slurm with the test dataset
+cruise run --mode slurm -profile test,biowulf
+

To run cruise on your own data, you'll need to create a sample sheet. Take a look at the example: assets/samplesheet_test.csv.

Once you've created a samplesheet with paths to your fastq files, run cruise with the --input option to specify the path to your sample sheet:

cruise run --mode slurm -profile biowulf --input samplesheet.csv
+

Help & Contributing

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.

References

This repo was originally generated from the CCBR Nextflow Template. The template takes inspiration from nektool1 and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow nf-core's instructions2.

Information on who the pipeline was developed for, and a statement if it's only been tested on Biowulf. For example:

It has been developed and tested solely on NIH HPC Biowulf.

Also include a workflow image to summarize the pipeline.


Last update: 2023-10-16
\ No newline at end of file diff --git a/nextflow/index.html b/nextflow/index.html new file mode 100644 index 0000000..d2e3b74 --- /dev/null +++ b/nextflow/index.html @@ -0,0 +1,5 @@ + nextflow pipeline - CRUISE

nextflow pipeline

You can run the nextflow pipeline directly by specifying this GitHub repo. You will need nextflow and either singularity or docker installed. In this case you don't need to run cruise init first, as the config files will be accessed directly from the GitHub repo.

nextflow run CCBR/CRUISE -profile test,singularity
+

You can specify a specific version, tag, or branch with -r:

nextflow run CCBR/CRUISE -r v1.0.0 -profile test,singularity
+

Create and use a custom reference genome:

nextflow run CCBR/CRUISE -profile test -entry MAKE_REFERENCE
+nextflow run CCBR/CRUISE -profile test -c results/test/genome/custom_genome.config
+

Last update: 2023-10-16
\ No newline at end of file diff --git a/release-guide/index.html b/release-guide/index.html new file mode 100644 index 0000000..05b6982 --- /dev/null +++ b/release-guide/index.html @@ -0,0 +1,16 @@ + Release Guide - CRUISE

Release Guide

How to test a pre-release on biowulf

Install the development version of cruise.

# activate the conda env for development
+. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
+conda activate py311
+
+# go to the source on biowulf and update
+cd /data/CCBR_Pipeliner/Pipelines/CRUISE/cruise-dev
+git pull
+# optionally switch to different branch if needed
+
+# install the version to a hidden path (e.g. .dev, .v1.0.0.9000) in /data/CCBR_Pipeliner/Pipelines/CRUISE
+cd ..
+pip install ./cruise-dev -t ./.dev
+# add it to your PATH and PYTHONPATH with:
+export PATH="$PATH:/data/CCBR_Pipeliner/Pipelines/CRUISE/.dev/bin/"
+export PYTHONPATH="$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CRUISE/.dev/"
+

Last update: 2023-10-16
\ No newline at end of file diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..9d5ddac --- /dev/null +++ b/requirements.txt @@ -0,0 +1,10 @@ +#https://pypi.org/project/mkdocs-git-revision-date-localized-plugin/ +mkdocs-git-revision-date-localized-plugin==1.2.0 +#https://pypi.org/project/mkdocs-minify-plugin/ +mkdocs-minify-plugin==0.6.4 +#https://pypi.org/project/mkdocs-git-revision-date-plugin/ +mkdocs-git-revision-date-plugin==0.3.2 +#https://pypi.org/project/mkdocs-material/ +mkdocs-material==9.1.6 +#https://pypi.org/project/mkdocs-material-extensions/ +mkdocs-material-extensions==1.1.1 diff --git a/search/search_index.json b/search/search_index.json new file mode 100644 index 0000000..76ce2ee --- /dev/null +++ b/search/search_index.json @@ -0,0 +1 @@ +{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Introduction","text":""},{"location":"#cruise","title":"CRUISE \ud83d\udef3\ufe0f","text":"

**C**rispr sc**R**een seq**U**encIng analy**S**is pip**E**line

\ud83d\udea7 This project is under active development. It is not yet ready for production use. \ud83d\udea7

"},{"location":"#set-up","title":"Set up","text":"

Cruise is installed on the Biowulf HPC. For installation in other execution environments, refer to the docs.

"},{"location":"#biowulf","title":"Biowulf","text":"

Cruise is available on Biowulf in the ccbrpipeliner module. You'll first need to start an interactive session and create a directory from where you'll run cruise.

# start an interactive node\nsinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200\n# make a working directory for your project and go to it\nmkdir -p /data/$USER/chipseq\ncd /data/$USER/chipseq\n# load the ccbrpipeliener module\nmodule load ccbrpipeliner\n
"},{"location":"#usage","title":"Usage","text":"

Initialize and run cruise with test data:

# copy the cruise config files to your current directory\ncruise init\n# preview the cruise jobs that will run with the test dataset\ncruise run --mode local -profile test -preview\n# launch a cruise run on slurm with the test dataset\ncruise run --mode slurm -profile test,biowulf\n

To run cruise on your own data, you'll need to create a sample sheet. Take a look at the example: assets/samplesheet_test.csv.

Once you've created a samplesheet with paths to your fastq files, run cruise with the --input option to specify the path to your sample sheet:

cruise run --mode slurm -profile biowulf --input samplesheet.csv\n
"},{"location":"#help-contributing","title":"Help & Contributing","text":"

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.

"},{"location":"#references","title":"References","text":"

This repo was originally generated from the CCBR Nextflow Template. The template takes inspiration from nektool1 and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow nf-core's instructions2.

Information on who the pipeline was developed for, and a statement if it's only been tested on Biowulf. For example:

It has been developed and tested solely on NIH HPC Biowulf.

Also include a workflow image to summarize the pipeline.

  1. nektool https://github.com/beardymcjohnface/nektool \u21a9

  2. instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core \u21a9

"},{"location":"changelog/","title":"Changelog","text":""},{"location":"changelog/#cruise-development-version","title":"CRUISE development version","text":""},{"location":"changelog/#new-features","title":"New features","text":"
  • Trim adapters with cutadapt.
  • Run mageck count. (#9)
  • mageck count only runs if a count table isn't given.
  • Optional: run mageck test and mle. (#9)
  • mageck mle only runs if a design matrix is given.
  • Optional: run drugZ. (#10)
  • Optional: run BAGEL2. (#11)
  • fc (fold change)
  • bf (bayes factor)
  • pr (precision recall)
  • CLI (#16)
  • cruise init to initialize a project directory.
  • cruise run
    • --mode slurm to submit a slurm job to biowulf or frce.
    • --main path/to/main.nf to select a different local install of cruise, or specify the repo (CCBR/CRUISE) to get it from GitHub.
"},{"location":"contributing/","title":"Contributing to CRUISE","text":"

TODO -- describe gitflow, require PRs...

"},{"location":"contributing/#use-pre-commit-hooks","title":"Use pre-commit hooks","text":"

Pre-commit can automatically format your code, check for spelling errors, etc. every time you commit.

Install pre-commit if you haven't already, then run pre-commit install to install the hooks specified in .pre-commit-config.yaml. Pre-commit will run the hooks every time you commit.

"},{"location":"contributing/#versions","title":"Versions","text":"

Increment the version number following semantic versioning1 in the VERSION file.

"},{"location":"contributing/#changelog","title":"Changelog","text":"

Keep the changelog up to date with all notable changes in CHANGELOG.md2.

"},{"location":"contributing/#vs-code-extensions","title":"VS code extensions","text":"

If you use VS code, installing nf-core extension pack is recommended.

"},{"location":"contributing/#installation","title":"Installation","text":"

For testing and debugging, We recommend installing the dev version of cruise to a user-specific location.

git clone https://github.com/CCBR/CRUISE\nmkdir -p ~/bin/cruise\npip install ./CRUISE -t ~/bin/cruise\nexport PATH=\"$HOME/bin/cruise/bin:$PATH\"\n
  1. semantic versioning guidelines https://semver.org/ \u21a9

  2. changelog guidelines: https://keepachangelog.com/en/1.1.0/ \u21a9

"},{"location":"getting-started/","title":"Getting Started with CRUISE","text":"

TODO intro paragraph

"},{"location":"getting-started/#installation","title":"Installation","text":"

CRUISE is installed on the Biowulf and FRCE clusters as part of the ccbrpipeliner module. If you'd like to run the pipeline in a different execution environment, take a look at how to run the nextflow pipeline directly.

"},{"location":"getting-started/#prepare-a-sample-sheet","title":"Prepare a sample sheet","text":"

TODO

"},{"location":"getting-started/#initialize","title":"Initialize","text":"

Copy the configuration files to your current working directory

cruise init\n
"},{"location":"getting-started/#run","title":"Run","text":"

TODO preview, stub, mode=slurm

TODO required params

Run preview to view processes that will run:

cruise run -profile test -preview\n

Launch a stub run to view processes that will run and download containers:

cruise run -profile test,singularity -stub\n

Run the test dataset using the test profile:

cruise run -profile test,singularity\n

or explicitly specify the output directory and input:

cruise run -profile singularity --outdir results/test --input assets/samplesheet_test.csv\n
"},{"location":"getting-started/#custom-reference-genome","title":"Custom reference genome","text":"

TODO different required params

Create and use a custom reference genome:

cruise run -profile test -entry MAKE_REFERENCE\ncruise run -profile test -c results/test/genome/custom_genome.config\n
"},{"location":"nextflow/","title":"nextflow pipeline","text":"

You can run the nextflow pipeline directly by specifying this GitHub repo. You will need nextflow and either singularity or docker installed. In this case you don't need to run cruise init first, as the config files will be accessed directly from the GitHub repo.

nextflow run CCBR/CRUISE -profile test,singularity\n

You can specify a specific version, tag, or branch with -r:

nextflow run CCBR/CRUISE -r v1.0.0 -profile test,singularity\n

Create and use a custom reference genome:

nextflow run CCBR/CRUISE -profile test -entry MAKE_REFERENCE\nnextflow run CCBR/CRUISE -profile test -c results/test/genome/custom_genome.config\n
"},{"location":"release-guide/","title":"Release Guide","text":""},{"location":"release-guide/#how-to-test-a-pre-release-on-biowulf","title":"How to test a pre-release on biowulf","text":"

Install the development version of cruise.

# activate the conda env for development\n. \"/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh\"\nconda activate py311\n\n# go to the source on biowulf and update\ncd /data/CCBR_Pipeliner/Pipelines/CRUISE/cruise-dev\ngit pull\n# optionally switch to different branch if needed\n\n# install the version to a hidden path (e.g. .dev, .v1.0.0.9000) in /data/CCBR_Pipeliner/Pipelines/CRUISE\ncd ..\npip install ./cruise-dev -t ./.dev\n# add it to your PATH and PYTHONPATH with:\nexport PATH=\"$PATH:/data/CCBR_Pipeliner/Pipelines/CRUISE/.dev/bin/\"\nexport PYTHONPATH=\"$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CRUISE/.dev/\"\n
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