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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Add ampliconstats process for all the files (Samtools development branch) #58

Open ac55-sanger opened 4 years ago

ac55-sanger commented 4 years ago

This feature of samtools is only available in it's development branch, hence it cannot be directly used. I have created a separate repo and updated the info in README.md file on how to build and use conda packages for htslib and samtools from their development branch. OR samtools entry can be removed from the enviroment.yml file and have the development branch installed manually.

This pull request generates ampliconstats on all the files in one go (as intended) by passing --ampliconstats flag to nextflow run command.

ac55-sanger commented 4 years ago

As this feature is available only on samtools development branch, anyone who wants to use it can follow below instructions:

  1. Install htslib and samtools as per instructions given below: https://github.com/samtools/htslib https://github.com/samtools/samtools

  2. Remove samtools entry from "environments/illumina/environment.yml" and "environments/extras.yml" files.

  3. Run the pipeline using instructions as per README file