--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: 2023-08-31
\ No newline at end of file
diff --git a/dev/search/search_index.json b/dev/search/search_index.json
index 5567c43..08e769d 100644
--- a/dev/search/search_index.json
+++ b/dev/search/search_index.json
@@ -1 +1 @@
-{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Home","text":""},{"location":"#crispin","title":"CRISPIN \ud83c\udf6a","text":"
CRISPr screen sequencing analysis pipelINe
formerly known as CRUISE
\ud83d\udea7 This project is under active development. It is not yet ready for production use. \ud83d\udea7
CRISPIN 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 crispin.
# 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/$USER/crisprseq\ncd /data/$USER/crisprseq\n# load the ccbrpipeliener module\nmodule load ccbrpipeliner\n
"},{"location":"#usage","title":"Usage","text":"
Initialize and run crispin with test data:
# copy the crispin config files to your current directory\ncrispin init\n# preview the crispin jobs that will run with the test dataset\ncrispin run --mode local -profile test -preview\n# launch a crispin run on slurm with the test dataset\ncrispin run --mode slurm -profile test,biowulf\n
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.
You'll also need to select an appropriate library for your dataset. CRISPIN is bundled with several libraries in assets/lib, or you can download your own. Once you've created a samplesheet with paths to your fastq files, run crispin with the --input option to specify the path to your sample sheet and --library for the path to your library file:
crispin run --mode slurm -profile biowulf --input samplesheet.csv --library assets/lib/yusa_library.csv\n
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.
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.
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 crispin init first, as the config files will be accessed directly from the GitHub repo.
nextflow run CCBR/CRISPIN -profile test,singularity\n
You can specify a specific version, tag, or branch with -r:
nextflow run CCBR/CRISPIN -r v1.0.0 -profile test,singularity\n
Create and use a custom reference genome:
nextflow run CCBR/CRISPIN -profile test -entry MAKE_REFERENCE\nnextflow run CCBR/CRISPIN -profile test -c results/test/genome/custom_genome.config\n
"}]}
\ No newline at end of file
+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Home","text":""},{"location":"#crispin","title":"CRISPIN \ud83c\udf6a","text":"
CRISPr screen sequencing analysis pipelINe
formerly known as CRUISE
\ud83d\udea7 This project is under active development. It is not yet ready for production use. \ud83d\udea7
CRISPIN 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 crispin.
# 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/$USER/crisprseq\ncd /data/$USER/crisprseq\n# load the ccbrpipeliener module\nmodule load ccbrpipeliner\n
"},{"location":"#usage","title":"Usage","text":"
Initialize and run crispin with test data:
# copy the crispin config files to your current directory\ncrispin init\n# preview the crispin jobs that will run with the test dataset\ncrispin run --mode local -profile test -preview\n# launch a crispin run on slurm with the test dataset\ncrispin run --mode slurm -profile test,biowulf\n
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.
You'll also need to select an appropriate library for your dataset. CRISPIN is bundled with several libraries in assets/lib, or you can download your own. Once you've created a samplesheet with paths to your fastq files, run crispin with the --input option to specify the path to your sample sheet and --library for the path to your library file:
crispin run --mode slurm -profile biowulf --input samplesheet.csv --library assets/lib/yusa_library.csv\n
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.
instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core \u21a9
"},{"location":"changelog/","title":"Changelog","text":""},{"location":"changelog/#crispin-development-version","title":"CRISPIN development version","text":""},{"location":"changelog/#crispin-100","title":"CRISPIN 1.0.0","text":"
The pipeline name has been changed from CRUISE \ud83d\udef3\ufe0f to CRISPIN \ud83c\udf6a. (#43, @kelly-sovacool)
Run spooker on workflow completion.
Print the recommended citation in bibtex format with crispin --citation. (#32, @kelly-sovacool)
Fix citation information (#38, @kelly-sovacool)
Improve the documentation website with a dropdown menu to select which version to view. The latest release is shown by default. (#45, @kelly-sovacool)
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.
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 crispin init first, as the config files will be accessed directly from the GitHub repo.
nextflow run CCBR/CRISPIN -profile test,singularity\n
You can specify a specific version, tag, or branch with -r:
nextflow run CCBR/CRISPIN -r v1.0.0 -profile test,singularity\n
Create and use a custom reference genome:
nextflow run CCBR/CRISPIN -profile test -entry MAKE_REFERENCE\nnextflow run CCBR/CRISPIN -profile test -c results/test/genome/custom_genome.config\n