chore: Merge branch 'main' of https://github.com/CCBR/CRUISE

.github/CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# Contributing to CRUISE
+# Contributing to CRISPIN
 
 TODO -- describe gitflow, require PRs...
 
@@ -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"
 ```

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -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
@@ -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)_

.github/ISSUE_TEMPLATE/config.yml

@@ -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.

.github/workflows/build.yml

@@ -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

CHANGELOG.md

@@ -1,7 +1,9 @@
 ## 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)
+- Print the recommended citation in bibtex format with `crispin --citation`. (#32, @kelly-sovacool)
+- Fix citation information (#38, @kelly-sovacool)
 
 ## CRUISE 0.1.1
 

CITATION.cff

@@ -1,18 +1,22 @@
 cff-version: 1.2.0
-message: "Please cite CRUISE as below:"
+message: "Please cite CRISPIN as below:"
 authors:
+  - family-names: Wong
+    given-names: Nathan
+    orcid: https://orcid.org/0000-0002-8882-3401
   - family-names: Sovacool
     given-names: Kelly
     orcid: https://orcid.org/0000-0003-3283-829X
-  - family-names: Wong
-    given-names: Nathan
   - family-names: Sevilla
     given-names: Samantha
     orcid: https://orcid.org/0000-0002-8734-9875
   - 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/CHAMPAGNE/
-repository-code: https://github.com/CCBR/CHAMPAGNE
+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
+date-released: 2023-11-06

README.md

@@ -1,21 +1,21 @@
-# CRUISE 🛳️
+# CRISPIN 🍪
 
-**C**rispr sc**R**een seq**U**encIng analy**S**is pip**E**line
+Crispr screen sequencing analysis pipeline
 
 🚧 **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).
+CRISPIN 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.
+CRISPIN 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 crispin.
 
 ```sh
 # start an interactive node
@@ -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).
 

bin/install_biowulf.sh

@@ -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"
@@ -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

conf/containers.config

@@ -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'

conf/test_mle.config

@@ -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

docker/README.md

@@ -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)

docker/bagel/README.md

@@ -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>

docker/bagel/meta.yml

@@ -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)"

docker/drugz/README.md

@@ -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>

docker/drugz/meta.yml

@@ -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)"

docs/getting-started.md

@@ -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).
@@ -18,7 +18,7 @@ TODO
 Copy the configuration files to your current working directory
 
 ```sh
-cruise init
+crispin init
 ```
 
 ## Run
@@ -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
@@ -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
 ```

docs/nextflow.md

@@ -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
 ```