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Arcadia-Science / seqqc

A Nextflow pipeline to identify quality control issues with new sequencing data.
MIT License
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documenting getting started with nf-core create #5

Open taylorreiter opened 2 years ago

taylorreiter commented 2 years ago

Zero to nf-core pipeline

mamba create -n nf nf-core nextflow prettier

nf-core create

? Workflow name seqqc
? Description Quality control for sequencing data
? Author Arcadia Science
? Do you want to customize which parts of the template are used? Yes
? Pipeline prefix Arcadia-Science
? Skip template areas? done 
  - github_badges
  - igenomes

nf-core lint
nf-core lint  --fix files_unchanged

git remote add origin git@github.com:USERNAME/REPO_NAME.git
git push --all origin

created a branch from master called main and switched default branch to main.

add modules

nf-core modules list remote
nf-core modules install sourmash/gather
nf-core modules install sourmash/sketch

(opened docker desktop) set up on rosetta, explicitly call for docker...

export DOCKER_DEFAULT_PLATFORM=linux/amd64
nextflow run . -profile test,docker --outdir outdir
elizabethmcd commented 2 years ago

A good place for this down the road could be the workflows-documentation site: https://arcadia-science.github.io/arcadia-workflows-documentation/ I have a placeholder page for instructions for how we go about creating templates so it is transparent and in a findable place, but that is probably for when we more decide on how we are going to standardize this process within the org

taylorreiter commented 2 years ago

ok! I just wanted to make sure i had something written down for how i started this repo. I'll keep the https://arcadia-science.github.io/arcadia-workflows-documentation/ in mind and add to it as we standardize!