Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/ccbr/ccbr_snakemaketemplate

Barebones framework for creating new snakemake workflows.

https://github.com/ccbr/ccbr_snakemaketemplate

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary

Keywords

snakemake techdev templates
Last synced: 9 months ago · JSON representation

Repository

Barebones framework for creating new snakemake workflows.

Basic Info
Statistics
  • Stars: 3
  • Watchers: 4
  • Forks: 1
  • Open Issues: 3
  • Releases: 0
Topics
snakemake techdev templates
Created over 5 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

CCBR Snakemake Pipeline Cookiecutter

This is a dummy folder framework for CCBR snakemake workflows. New workflows can be started using this repository as a template.

Creating PAT for GH

This is a prerequisite for the next step. You will need gh cli installed on your laptop or use /data/CCBR_Pipeliner/db/PipeDB/bin/gh_1.7.0_linux_amd64/bin/gh on biowulf. Skip if can access github in an automated way already.

Personal Access Token (PAT) is required to access GitHub (GH) without having to authenticate by other means (like password) every single time. You can create a PAT by going here. Then you can copy the PAT and save it into a file on biowulf (say ~/gh_token). Next, you can run the following command to set everything up correctly on biowulf (or your laptop) gh auth login --with-token < ~/git_token

Creating new repository

You can use gh cli to * create a new repository under CCBR, and * copy over the template code from CCBRSnakemakePipelineCookiecutter with the following command ``` gh repo create CCBR/ \ --description "" \ --public \ --template CCBR/CCBRSnakemakePipelineCookiecutter \ --confirm `` On biowulf, you may have to specify the full path of theghexecutable is located here:/data/CCBRPipeliner/db/PipeDB/bin/gh1.7.0linuxamd64/bin/gh`

Then you can clone a local copy of the new repository: gh repo clone CCBR/<reponame>.git

If you drop the CCBR/ from the gh command above, then the new repo is created under your username. The commands would then look like this: ``` gh repo create \ --description "" \ --public \ --template CCBR/CCBR_SnakemakePipelineCookiecutter \ --confirm

gh repo clone /.git ```

You can change --public to --private in the above gh command to make the newly created repository private.

Owner

  • Name: CCR Collaborative Bioinformatics Resource
  • Login: CCBR
  • Kind: organization
  • Email: nciccbr@mail.nih.gov
  • Location: United States of America

CCR Collaborative Bioinformatics Resource, Center for Cancer Research (NCI), National Institutes of Health

GitHub Events

Total
  • Issues event: 1
  • Delete event: 1
  • Push event: 1
  • Pull request event: 3
  • Create event: 1
Last Year
  • Issues event: 1
  • Delete event: 1
  • Push event: 1
  • Pull request event: 3
  • Create event: 1

Dependencies

.github/workflows/build_mkdocs.yaml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/lintr.yaml actions
  • actions/checkout v2 composite
  • docker://snakemake/snakemake v7.19.1 composite
.github/workflows/techdev-project.yml actions
  • actions/add-to-project v1.0.2 composite
.github/workflows/test_dev.yml actions
  • docker://snakemake/snakemake v7.19.1 composite
.github/workflows/user-projects.yml actions
docs/requirements.txt pypi
  • mkdocs-git-revision-date-localized-plugin ==1.2.0
  • mkdocs-git-revision-date-plugin ==0.3.2
  • mkdocs-material ==9.1.6
  • mkdocs-material-extensions ==1.1.1
  • mkdocs-minify-plugin ==0.6.4