nf-star

Create the test directory:

mkdir -p ~/nf-star-test/raw_data

Download the demo data:

cd ~/nf-star-test/raw_data
curl -J -O https://datashare.mpcdf.mpg.de/s/jcEaS5vqpJO0lOy/download
curl -J -O https://datashare.mpcdf.mpg.de/s/XHanbnjfvQ9rACD/download
curl -J -O https://datashare.mpcdf.mpg.de/s/sIebkRdMfMSweq2/download
curl -J -O https://datashare.mpcdf.mpg.de/s/zoNxS9vRI7jl77y/download
curl -J -O https://datashare.mpcdf.mpg.de/s/0WHGNIhjJC792lY/download
curl -J -O https://datashare.mpcdf.mpg.de/s/ZlM0lWKPh8KrP6B/download
curl -J -O https://datashare.mpcdf.mpg.de/s/o3O6BKaEXqB7TTo/download

Download the paramaters file:

cd ~/nf-star-test
curl -J -O https://raw.githubusercontent.com/mpg-age-bioinformatics/nf-star/main/params.json

Run the workflow:

nextflow run nf-star -params-file nf-star/params.json -entry images -profile studio && \
nextflow run nf-star -params-file nf-star/params.json -entry rename -profile studio && \
nextflow run nf-star -params-file nf-star/params.json -entry index -profile studio && \
nextflow run nf-star -params-file nf-star/params.json -entry bam_index -profile studio && \
nextflow run nf-star -params-file nf-star/params.json -entry map_reads -profile studio && \
nextflow run nf-star -params-file nf-star/params.json -entry merging -profile studio

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Contributing

Make a commit, check the last tag, add a new one, push it and make a release:

git add -A . && git commit -m "<message>" && git push
git describe --abbrev=0 --tags
git tag -e -a <tag> HEAD
git push origin --tags
gh release create <tag> 

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