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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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nextflow run on main branch #3

Closed elizabethmcd closed 1 year ago

elizabethmcd commented 1 year ago

Out of curiosity after reviewing the recent PR I wanted to test the pipeline with nextflow run Arcadia-Science/seqqc -profile test,docker --outdir test and got the error: 

Project `Arcadia-Science/seqqc` is currently stickied on revision: main -- you need to explicitly specify a revision with the option `-r` in order to use it

Using the command nextflow run Arcadia-Science/seqqc -profile test,docker -outdir test -r main fixes this.

However, this will either affect how we create templates or put in the documentation how to run the pipeline. Either:

  1. Go back to master branch convention since that's how nf-core create makes pipelines and evidently how nextflow run expects it
  2. Just write in the documentation to include the -r main flag
taylorreiter commented 1 year ago

I switched the default branch back to master because I don't want to deal with switching over all of the failed linting.