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Merge pull request #43 from CCBR/rename
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Rename the pipeline to CRISPIN
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kopardev authored May 6, 2024
2 parents b668537 + 0a02a2a commit 1deda04
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12 changes: 6 additions & 6 deletions .github/CONTRIBUTING.md
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@@ -1,4 +1,4 @@
# Contributing to CRUISE
# Contributing to CRISPIN

TODO -- describe gitflow, require PRs...

Expand Down Expand Up @@ -28,11 +28,11 @@ If you use VS code, installing [nf-core extension pack](https://marketplace.visu

## Installation

For testing and debugging, We recommend installing the dev version of cruise to a user-specific location.
For testing and debugging, We recommend installing the dev version of crispin 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"
git clone https://github.com/CCBR/CRISPIN
mkdir -p ~/bin/crispin
pip install ./CRISPIN -t ~/bin/crispin
export PATH="$HOME/bin/crispin/bin:$PATH"
```
4 changes: 2 additions & 2 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -7,7 +7,7 @@ body:
value: |
Before you post this issue, please check the documentation:
- [pipeline documentation: troubleshooting](https://ccbr.github.io/CRUISE/user-guide/troubleshooting/)
- [pipeline documentation: troubleshooting](https://ccbr.github.io/CRISPIN/user-guide/troubleshooting/)
- type: textarea
id: description
Expand Down Expand Up @@ -47,4 +47,4 @@ body:
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity)_
* OS _(eg. Ubuntu Linux, macOS)_
* Version of CCBR/CRUISE _(eg. 1.0, 1.8.2)_
* Version of CCBR/CRISPIN _(eg. 1.0, 1.8.2)_
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/config.yml
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@@ -1,4 +1,4 @@
contact_links:
- name: CCBR Discussions
url: https://github.com/CCBR/CRUISE/discussions
url: https://github.com/CCBR/CRISPIN/discussions
about: Please ask and answer questions here.
12 changes: 6 additions & 6 deletions .github/workflows/build.yml
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Expand Up @@ -30,17 +30,17 @@ jobs:
run: |
python -m pip install --upgrade pip setuptools
pip install .[dev,test]
python -c 'from cruise.src.util import chmod_bins_exec; chmod_bins_exec()'
python -c 'from crispin.src.util import chmod_bins_exec; chmod_bins_exec()'
- name: Check CLI basics
run: |
which cruise
cruise --version
cruise --citation
which crispin
crispin --version
crispin --citation
- name: Test stub run
run: |
cd tests/
cruise init
cruise run -profile ci_stub -stub
crispin init
crispin run -profile ci_stub -stub
build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
runs-on: ubuntu-latest
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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@@ -1,7 +1,8 @@
## development version

- The pipeline name has been changed from CRUISE 🛳️ to CRISPIN 🍪. (#43, @kelly-sovacool)
- Run spooker on workflow completion.
- Print the recommended citation in bibtex format with `cruise --citation`. (#32, @kelly-sovacool)
- Print the recommended citation in bibtex format with `crispin --citation`. (#32, @kelly-sovacool)
- Fix citation information (#38, @kelly-sovacool)

## CRUISE 0.1.1
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8 changes: 4 additions & 4 deletions CITATION.cff
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@@ -1,5 +1,5 @@
cff-version: 1.2.0
message: "Please cite CRUISE as below:"
message: "Please cite CRISPIN as below:"
authors:
- family-names: Wong
given-names: Nathan
Expand All @@ -13,9 +13,9 @@ authors:
- family-names: Koparde
given-names: Vishal
orcid: https://orcid.org/0000-0001-8978-8495
title: "CRUISE: Crispr scReen seqUencIng analySis pipEline"
url: https://ccbr.github.io/CRUISE
repository-code: https://github.com/CCBR/CRUISE
title: "CRISPIN: CRISPR screen pipeline"
url: https://ccbr.github.io/CRISPIN
repository-code: https://github.com/CCBR/CRISPIN
license: MIT
type: software
version: v0.1.1
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36 changes: 18 additions & 18 deletions README.md
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@@ -1,21 +1,21 @@
# CRUISE 🛳️
# CRISPIN 🍪

**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](https://github.com/CCBR/CRUISE/actions/workflows/build.yml/badge.svg)](https://github.com/CCBR/CRUISE/actions/workflows/build.yml)
[![build](https://github.com/CCBR/CRISPIN/actions/workflows/build.yml/badge.svg)](https://github.com/CCBR/CRISPIN/actions/workflows/build.yml)

## Set up

Cruise is installed on the [Biowulf HPC](#biowulf).
For installation in other execution environments,
refer to the [docs](https://ccbr.github.io/cruise).
refer to the [docs](https://ccbr.github.io/crispin).

### Biowulf

Cruise is available on [Biowulf](https://hpc.nih.gov/) in the `ccbrpipeliner` module.
You'll first need to start an interactive session and create a directory from where you'll run cruise.
You'll first need to start an interactive session and create a directory from where you'll run crispin.

```sh
# start an interactive node
Expand All @@ -29,37 +29,37 @@ module load ccbrpipeliner

## Usage

Initialize and run cruise with test data:
Initialize and run crispin with test data:

```sh
# 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
# copy the crispin config files to your current directory
crispin init
# preview the crispin jobs that will run with the test dataset
crispin run --mode local -profile test -preview
# launch a crispin run on slurm with the test dataset
crispin 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:
To run crispin on your own data, you'll need to create a sample sheet.
Take a look at the example:
[assets/samplesheet_test_biowulf.csv](assets/samplesheet_test_biowulf.csv).

You'll also need to select an appropriate library for your dataset.
CRUISE is bundled with several libraries in [assets/lib](assets/lib),
CRISPIN is bundled with several libraries in [assets/lib](assets/lib),
or you can download your own.
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
run crispin with the `--input` option to specify the path to your sample sheet
and `--library` for the path to your library file:

```sh
cruise run --mode slurm -profile biowulf --input samplesheet.csv --library assets/lib/yusa_library.csv
crispin run --mode slurm -profile biowulf --input samplesheet.csv --library assets/lib/yusa_library.csv
```

## Help & Contributing

Come across a **bug**? Open an [issue](https://github.com/CCBR/CRUISE/issues) and include a minimal reproducible example.
Come across a **bug**? Open an [issue](https://github.com/CCBR/CRISPIN/issues) and include a minimal reproducible example.

Have a **question**? Ask it in [discussions](https://github.com/CCBR/CRUISE/discussions).
Have a **question**? Ask it in [discussions](https://github.com/CCBR/CRISPIN/discussions).

Want to **contribute** to this project? Check out the [contributing guidelines](docs/CONTRIBUTING.md).

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4 changes: 2 additions & 2 deletions assets/samplesheet_test_biowulf.csv

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2 changes: 1 addition & 1 deletion assets/slurm_header_biowulf.sh

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2 changes: 1 addition & 1 deletion assets/slurm_header_frce.sh

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8 changes: 4 additions & 4 deletions bin/install_biowulf.sh
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Expand Up @@ -3,9 +3,9 @@
# bin/install_biowulf.sh
set -euxo pipefail

repo_path=/data/CCBR_Pipeliner/Pipelines/CRUISE/dev/
repo_path=/data/CCBR_Pipeliner/Pipelines/CRISPIN/dev/
version=`cat ${repo_path}/VERSION`
install_path=/data/CCBR_Pipeliner/Pipelines/CRUISE/.${version}
install_path=/data/CCBR_Pipeliner/Pipelines/CRISPIN/.${version}
bin_path=${install_path}/bin/

. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
Expand All @@ -16,9 +16,9 @@ pushd ${repo_path}
rm -rf build/ *.egg-info
popd

echo "Installing CRUISE to ${install_path}"
echo "Installing CRISPIN to ${install_path}"
pip install ${repo_path} --target ${install_path} --upgrade
chmod a+rx ${install_path}/cruise/bin/*.*
chmod a+rx ${install_path}/crispin/bin/*.*
chmod -R a+r ${install_path}

if [[ ":$PATH:" != *":${bin_path}:"* ]];then
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4 changes: 2 additions & 2 deletions conf/containers.config
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@@ -1,10 +1,10 @@
// containers accessed in process definitions with $params.containers.NAME
params {
containers {
bagel = 'nciccbr/cruise_bagel_2.0:0.1.0'
bagel = 'nciccbr/crispin_bagel_2.0:0.1.0'
base = 'nciccbr/ccbr_ubuntu_base_20.04:v5'
cutadapt = 'nciccbr/ncigb_cutadapt_v1.18:latest'
drugz = 'nciccbr/cruise_drugz:0.1.0'
drugz = 'nciccbr/crispin_drugz:0.1.0'
fastqc = 'nciccbr/ccrgb_qctools:v4.0'
mageck = 'quay.io/biocontainers/mageck:0.5.9.5--py39h1f90b4d_3'
vispr = 'quay.io/biocontainers/mageck-vispr:0.5.6--py_0'
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4 changes: 2 additions & 2 deletions conf/test_mle.config
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Expand Up @@ -7,8 +7,8 @@ params {
outdir = 'results/test_mle'
exp_name = 'leukemia'

count_table = '/data/CCBR_Pipeliner/testdata/CRUISE/leukemia.new.csv'
design_matrix = '/data/CCBR_Pipeliner/testdata/CRUISE/designmat.txt'
count_table = '/data/CCBR_Pipeliner/testdata/CRISPIN/leukemia.new.csv'
design_matrix = '/data/CCBR_Pipeliner/testdata/CRISPIN/designmat.txt'

mageck.run = true
drugz.run = false
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4 changes: 2 additions & 2 deletions docker/README.md
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@@ -1,6 +1,6 @@
# Containers for CRUISE
# Containers for CRISPIN

Dockerfiles to create containers for processes in this nextflow workflow.
These containers are built and pushed to dockerhub automatically when files in this directory change.

[![docker](https://github.com/CCBR/CRUISE/actions/workflows/docker.yml/badge.svg)](https://github.com/CCBR/CRUISE/actions/workflows/docker.yml)
[![docker](https://github.com/CCBR/CRISPIN/actions/workflows/docker.yml/badge.svg)](https://github.com/CCBR/CRISPIN/actions/workflows/docker.yml)
4 changes: 2 additions & 2 deletions docker/bagel/README.md
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@@ -1,5 +1,5 @@
# bagel

Container for bagel processes in CRUISE
Container for bagel processes in CRISPIN

<https://hub.docker.com/r/nciccbr/cruise_bagel_2.0>
<https://hub.docker.com/r/nciccbr/crispin_bagel_2.0>
2 changes: 1 addition & 1 deletion docker/bagel/meta.yml
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@@ -1,4 +1,4 @@
dockerhub_namespace: nciccbr
image_name: cruise_bagel_2.0
image_name: crispin_bagel_2.0
version: 0.1.0
container: "$(dockerhub_namespace)/$(image_name):$(version)"
4 changes: 2 additions & 2 deletions docker/drugz/README.md
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@@ -1,5 +1,5 @@
# drugZ

Container for drugZ processes in CRUISE
Container for drugZ processes in CRISPIN

<https://hub.docker.com/r/nciccbr/cruise_drugz>
<https://hub.docker.com/r/nciccbr/crispin_drugz>
2 changes: 1 addition & 1 deletion docker/drugz/meta.yml
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@@ -1,4 +1,4 @@
dockerhub_namespace: nciccbr
image_name: cruise_drugz
image_name: crispin_drugz
version: 0.1.0
container: "$(dockerhub_namespace)/$(image_name):$(version)"
18 changes: 9 additions & 9 deletions docs/getting-started.md
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@@ -1,10 +1,10 @@
# Getting Started with CRUISE
# Getting Started with CRISPIN

TODO intro paragraph

## Installation

CRUISE is installed on the Biowulf and FRCE clusters as part of the
CRISPIN 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](nextflow.md).
Expand All @@ -18,7 +18,7 @@ TODO
Copy the configuration files to your current working directory

```sh
cruise init
crispin init
```

## Run
Expand All @@ -30,25 +30,25 @@ TODO required params
Run preview to view processes that will run:

```sh
cruise run -profile test -preview
crispin run -profile test -preview
```

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

```sh
cruise run -profile test,singularity -stub
crispin run -profile test,singularity -stub
```

Run the test dataset using the test profile:

```sh
cruise run -profile test,singularity
crispin run -profile test,singularity
```

or explicitly specify the output directory and input:

```sh
cruise run -profile singularity --outdir results/test --input assets/samplesheet_test.csv
crispin run -profile singularity --outdir results/test --input assets/samplesheet_test.csv
```

### Custom reference genome
Expand All @@ -58,6 +58,6 @@ TODO different required params
Create and use a custom reference genome:

```sh
cruise run -profile test -entry MAKE_REFERENCE
cruise run -profile test -c results/test/genome/custom_genome.config
crispin run -profile test -entry MAKE_REFERENCE
crispin run -profile test -c results/test/genome/custom_genome.config
```
10 changes: 5 additions & 5 deletions docs/nextflow.md
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Expand Up @@ -2,22 +2,22 @@

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,
In this case you don't need to run `crispin init` first,
as the config files will be accessed directly from the GitHub repo.

```sh
nextflow run CCBR/CRUISE -profile test,singularity
nextflow run CCBR/CRISPIN -profile test,singularity
```

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

```sh
nextflow run CCBR/CRUISE -r v1.0.0 -profile test,singularity
nextflow run CCBR/CRISPIN -r v1.0.0 -profile test,singularity
```

Create and use a custom reference genome:

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