So this is a first pass PR that updates the template code for the pipeline to version 1.6. We will need to do this at some point anyway for the creation of the TEMPLATE branch for the automated template code syncing:
https://nf-co.re/developers/sync
Removed any bits that were specific to the Crick although there are still a couple of places these exist - I have left the more important bits in for now until we have the containers and test-dataset sorted.
Added pipeline logo to main README and to completion email
I havent looked at the processes themselves but we can address these changes in another PR.
Have a look at the changes and make any comments/suggestions if you want me to change anything. Then when you are happy with the changes just merge the pull request. Once merged the pipeline will require testing because I have no way of using automated tests at the moment until we set-up a test-dataset.
Many thanks to contributing to nf-core/demultiplex!
Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
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nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/demultiplex/tree/master/.github/CONTRIBUTING.md
Hi @csawye01 !
So this is a first pass PR that updates the template code for the pipeline to version
1.6. We will need to do this at some point anyway for the creation of theTEMPLATEbranch for the automated template code syncing: https://nf-co.re/developers/syncI havent looked at the processes themselves but we can address these changes in another PR.
Have a look at the changes and make any comments/suggestions if you want me to change anything. Then when you are happy with the changes just merge the pull request. Once merged the pipeline will require testing because I have no way of using automated tests at the moment until we set-up a test-dataset.