diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index ae0dcbd..e4dc4ed 100644 --- a/.github/CONTRIBUTING.md +++ b/.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" ``` diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index e083872..7e6196e 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.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)_ diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index f6ff88a..985fb66 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.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. diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 5963053..42080d9 100644 --- a/.github/workflows/build.yml +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index 4367584..a9f703d 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/CITATION.cff b/CITATION.cff index 5c8f3f2..d9b340a 100644 --- a/CITATION.cff +++ b/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 diff --git a/README.md b/README.md index 7813269..20723f1 100644 --- a/README.md +++ b/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). diff --git a/assets/samplesheet_test_biowulf.csv b/assets/samplesheet_test_biowulf.csv index e77f08e..2f7f3e4 100644 --- a/assets/samplesheet_test_biowulf.csv +++ b/assets/samplesheet_test_biowulf.csv @@ -1,3 +1,3 @@ sample,fastq_1,fastq_2,treat_or_ctrl -plasmid,/data/CCBR_Pipeliner/testdata/CRUISE/ERR376998.fastq.gz,,control -ESC1,/data/CCBR_Pipeliner/testdata/CRUISE/ERR376999.fastq.gz,,treatment +plasmid,/data/CCBR_Pipeliner/testdata/CRISPIN/ERR376998.fastq.gz,,control +ESC1,/data/CCBR_Pipeliner/testdata/CRISPIN/ERR376999.fastq.gz,,treatment diff --git a/assets/slurm_header_biowulf.sh b/assets/slurm_header_biowulf.sh index c63a778..f9a599e 100644 --- a/assets/slurm_header_biowulf.sh +++ b/assets/slurm_header_biowulf.sh @@ -3,7 +3,7 @@ #SBATCH --mem=1g #SBATCH --time=1-00:00:00 #SBATCH --parsable -#SBATCH -J "CRUISE" +#SBATCH -J "CRISPIN" #SBATCH --mail-type=BEGIN,END,FAIL #SBATCH --output "log/slurm_%j.log" #SBATCH --output "log/slurm_%j.log" diff --git a/assets/slurm_header_frce.sh b/assets/slurm_header_frce.sh index 5441095..09acda8 100644 --- a/assets/slurm_header_frce.sh +++ b/assets/slurm_header_frce.sh @@ -3,7 +3,7 @@ #SBATCH --mem=1g #SBATCH --time=1-00:00:00 #SBATCH --parsable -#SBATCH -J "CRUISE" +#SBATCH -J "CRISPIN" #SBATCH --mail-type=BEGIN,END,FAIL #SBATCH --output "log/slurm_%j.log" #SBATCH --output "log/slurm_%j.log" diff --git a/bin/install_biowulf.sh b/bin/install_biowulf.sh index e91acf6..0caafb1 100755 --- a/bin/install_biowulf.sh +++ b/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 diff --git a/conf/containers.config b/conf/containers.config index c552834..803dca6 100644 --- a/conf/containers.config +++ b/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' diff --git a/conf/test_mle.config b/conf/test_mle.config index 0e6ce55..687e226 100644 --- a/conf/test_mle.config +++ b/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 diff --git a/docker/README.md b/docker/README.md index c63c58f..5561618 100644 --- a/docker/README.md +++ b/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) diff --git a/docker/bagel/README.md b/docker/bagel/README.md index 18f066e..3c38d0d 100644 --- a/docker/bagel/README.md +++ b/docker/bagel/README.md @@ -1,5 +1,5 @@ # bagel -Container for bagel processes in CRUISE +Container for bagel processes in CRISPIN - + diff --git a/docker/bagel/meta.yml b/docker/bagel/meta.yml index 7b4b867..cd60523 100644 --- a/docker/bagel/meta.yml +++ b/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)" diff --git a/docker/drugz/README.md b/docker/drugz/README.md index 64f676b..edf9c21 100644 --- a/docker/drugz/README.md +++ b/docker/drugz/README.md @@ -1,5 +1,5 @@ # drugZ -Container for drugZ processes in CRUISE +Container for drugZ processes in CRISPIN - + diff --git a/docker/drugz/meta.yml b/docker/drugz/meta.yml index f8dedb5..c08503c 100644 --- a/docker/drugz/meta.yml +++ b/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)" diff --git a/docs/getting-started.md b/docs/getting-started.md index 7095d68..33ebd4c 100644 --- a/docs/getting-started.md +++ b/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 ``` diff --git a/docs/nextflow.md b/docs/nextflow.md index 6bddf24..4aa37b7 100644 --- a/docs/nextflow.md +++ b/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 ``` diff --git a/docs/release-guide.md b/docs/release-guide.md index 71e579d..0372e91 100644 --- a/docs/release-guide.md +++ b/docs/release-guide.md @@ -2,7 +2,7 @@ ## How to test a pre-release on biowulf -Install the development version of cruise. +Install the development version of crispin. ```sh # activate the conda env for development @@ -10,28 +10,28 @@ Install the development version of cruise. conda activate py311 # go to the source on biowulf and update -cd /data/CCBR_Pipeliner/Pipelines/CRUISE/cruise-dev +cd /data/CCBR_Pipeliner/Pipelines/CRISPIN/crispin-dev git pull # optionally switch to different branch if needed -# install the version to a hidden path (e.g. .v0.1.0, .v1.0.0.9000) in /data/CCBR_Pipeliner/Pipelines/CRUISE +# install the version to a hidden path (e.g. .v0.1.0, .v1.0.0.9000) in /data/CCBR_Pipeliner/Pipelines/CRISPIN cd .. -pip install ./cruise-dev -t ./.v0.1.0 +pip install ./crispin-dev -t ./.v0.1.0 # add it to your PATH and PYTHONPATH with: -export PATH="$PATH:/data/CCBR_Pipeliner/Pipelines/CRUISE/.v0.1.0/bin/" -export PYTHONPATH="$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CRUISE/.v0.1.0/" +export PATH="$PATH:/data/CCBR_Pipeliner/Pipelines/CRISPIN/.v0.1.0/bin/" +export PYTHONPATH="$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CRISPIN/.v0.1.0/" ``` -## Add CRUISE to the ccbrpipeliner module on biowulf +## Add CRISPIN to the ccbrpipeliner module on biowulf Create a lua file in `/data/CCBR_Pipeliner/modules/ccbrpipeliner`, e.g. `dev.lua`. You can copy the most recent lua file to use as a base, then modify the following line: ```lua -source_sh("bash", "/data/CCBR_Pipeliner/Pipelines/CRUISE/cruise-dev/bin/install.sh .v0.1.0") +source_sh("bash", "/data/CCBR_Pipeliner/Pipelines/CRISPIN/crispin-dev/bin/install.sh .v0.1.0") ``` -Change the version of CRUISE as needed. Notice the dot (`.`) in front of the version number to indicate a hidden path. +Change the version of CRISPIN as needed. Notice the dot (`.`) in front of the version number to indicate a hidden path. Then use and load the module (substitute `dev` for whatever you named the new lua file) with: diff --git a/main.nf b/main.nf index 99e2b99..b2d4d30 100644 --- a/main.nf +++ b/main.nf @@ -1,5 +1,5 @@ log.info """\ -CRUISE 🛳️ +CRISPIN 🍪 ============= NF version : $nextflow.version runName : $workflow.runName diff --git a/mkdocs.yml b/mkdocs.yml index 02766c4..5c01d12 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,12 +1,12 @@ # Project Information -site_name: CRUISE +site_name: CRISPIN site_author: CCR Collaborative Bioinformatics Resource site_description: >- - insert a one-line description of CRUISE here + insert a one-line description of CRISPIN here # Repository -repo_name: CCBR/CRUISE -repo_url: https://github.com/CCBR/CRUISE -edit_uri: https://github.com/CCBR/CRUISE/edit/main/ +repo_name: CCBR/CRISPIN +repo_url: https://github.com/CCBR/CRISPIN +edit_uri: https://github.com/CCBR/CRISPIN/edit/main/ # Copyright copyright: Copyright © 2023 CCR Collaborative Bioinformatics Resource diff --git a/modules.json b/modules.json index a006ca4..8355d6d 100644 --- a/modules.json +++ b/modules.json @@ -1,6 +1,6 @@ { - "name": "CCBR/CRUISE", - "homePage": "https://github.com/CCBR/CRUISE", + "name": "CCBR/CRISPIN", + "homePage": "https://github.com/CCBR/CRISPIN", "repos": { "https://github.com/CCBR/nf-modules": { "modules": { diff --git a/nextflow.config b/nextflow.config index df4f12b..2e6ebb4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -4,7 +4,7 @@ params { input = null library = null outdir = 'results' - exp_name = 'cruise' + exp_name = 'crispin' count_table = null design_matrix = null @@ -104,10 +104,10 @@ report { includeConfig 'conf/modules.config' manifest { - name = "CCBR/CRUISE" + name = "CCBR/CRISPIN" author = "CCR Collaborative Bioinformatics Resource" - homePage = "https://github.com/CCBR/CRUISE" - description = "Crispr scReen seqUencIng analySis pipEline" + homePage = "https://github.com/CCBR/CRISPIN" + description = "CRISPR screen pipeline" mainScript = "main.nf" } diff --git a/pyproject.toml b/pyproject.toml index d967153..9eec210 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,9 +6,9 @@ requires = [ build-backend = 'setuptools.build_meta' [project] -name = 'CRUISE' +name = 'CRISPIN' dynamic = ['version','readme'] -description = "TODO insert description of CRUISE here" +description = "TODO insert description of CRISPIN here" keywords = ["bioinformatics", "nextflow"] authors = [ {name = "Kelly Sovacool", email = "kelly.sovacool@nih.gov"}, @@ -51,16 +51,16 @@ test = [ ] [project.scripts] -cruise = "cruise.src.__main__:main" +crispin = "crispin.src.__main__:main" [project.urls] -Homepage = "https://ccbr.github.io/CRUISE" -Documentation = "https://ccbr.github.io/CRUISE" -Repository = "https://github.com/CCBR/CRUISE" -Changelog = "https://github.com/CCBR/CRUISE/blob/main/docs/CHANGELOG.md" +Homepage = "https://ccbr.github.io/CRISPIN" +Documentation = "https://ccbr.github.io/CRISPIN" +Repository = "https://github.com/CCBR/CRISPIN" +Changelog = "https://github.com/CCBR/CRISPIN/blob/main/docs/CHANGELOG.md" [tool.setuptools.package-dir] -cruise = "." +crispin = "." [tool.setuptools.package-data] "*" = ["CITATION.cff", "LICENSE", "VERSION", "main.nf", "nextflow.config", "assets/**", "assets/**", "bin/**", "conf/**", "modules/**", "subworkflows/**"] diff --git a/src/__main__.py b/src/__main__.py index 2847ec1..97ba7da 100644 --- a/src/__main__.py +++ b/src/__main__.py @@ -1,5 +1,5 @@ """ -Entrypoint for CRUISE CLI +Entrypoint for CRISPIN CLI Check out the wiki for a detailed look at customizing this file: https://github.com/beardymcjohnface/Snaketool/wiki/Customising-your-Snaketool @@ -40,10 +40,14 @@ def common_options(func): help="Print the citation in bibtex format and exit.", ) def cli(): - """Crispr scReen seqUencIng analySis pipEline + """CRISPR screen pipeline For more options, run: - cruise [command] --help""" + crispin [command] --help + + See the docs website for more details: + https://ccbr.github.io/CRISPIN/ + """ pass @@ -51,15 +55,18 @@ def cli(): \b EXAMPLES: Execute with slurm: - cruise run ... --mode slurm + crispin run ... --mode slurm Preview the processes that will run: - cruise run ... --mode local -preview + crispin run ... --mode local -preview Add nextflow args (anything supported by `nextflow run`): - cruise run ... -work-dir path/to/workDir -Run with a specific installation of cruise: - cruise run --main path/to/cruise/main.nf ... + crispin run ... -work-dir path/to/workDir +Run with a specific installation of crispin: + crispin run --main path/to/crispin/main.nf ... Run with a specific tag, branch, or commit from GitHub: - cruise run --main CCBR/CRUISE -r v0.1.0 ... + crispin run --main CCBR/CRISPIN -r v0.1.0 ... + +See the docs website for more details: +https://ccbr.github.io/CRISPIN/ """ @@ -72,7 +79,7 @@ def cli(): @click.option( "--main", "main_path", - help="Path to the cruise main.nf file or the GitHub repo (CCBR/CRUISE). Defaults to the version installed in the $PATH.", + help="Path to the crispin main.nf file or the GitHub repo (CCBR/CRISPIN). Defaults to the version installed in the $PATH.", type=str, default=nek_base(os.path.join("main.nf")), show_default=True, @@ -88,13 +95,13 @@ def cli(): @common_options def run(main_path, _mode, **kwargs): """Run the workflow""" - if ( # this is the only acceptable github repo option for cruise - main_path != "CCBR/CRUISE" + if ( # this is the only acceptable github repo option for crispin + main_path != "CCBR/CRISPIN" ): # make sure the path exists if not os.path.exists(main_path): raise FileNotFoundError( - f"Path to the cruise main.nf file not found: {main_path}" + f"Path to the crispin main.nf file not found: {main_path}" ) run_nextflow(