TheJacksonLaboratory / splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline
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Fixes containers and parametrizes options in google.config #281

Closed Vlad-Dembrovskyi closed 3 years ago

Vlad-Dembrovskyi commented 3 years ago

This PR

To test

git clone https://github.com/TheJacksonLaboratory/splicing-pipelines-nf
cd splicing-pipelines-nf
nextflow run . --reads examples/testdata/sra/sra.csv --singleEnd --download_from SRA --gtf https://lifebit-featured-datasets.s3-eu-west-1.amazonaws.com/projects/jax/splicing-pipelines-nf/genes.gtf --star_index https://lifebit-featured-datasets.s3-eu-west-1.amazonaws.com/projects/jax/splicing-pipelines-nf/star_2.7.9a_yeast_chr_I.tar.gz --test true --readlength 500 --overhang 100 --max_cpus 2 --max_memory 6.GB --max_time 48.h

Successful CloudOS run

https://cloudos.lifebit.ai/app/jobs/6168145e1b866a01d698f3ca https://cloudos.lifebit.ai/public/jobs/6168145e1b866a01d698f3ca (public)