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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 samtools ampliconstats feature #53

Closed ac55-sanger closed 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.

This pull request also generates ampliconstats per file basis. Will soon add support to run it against all the files in one go.

sb10 commented 4 years ago

Since this requires special installation for dev samtools, if that can't be integrated cleanly into this repo, ampliconstats will need to be made an option, so it doesn't break the existing tests. Ideally a test should be added for ampliconstats mode, if it's possible to install dev samtools as part of the test script.

ac55-sanger commented 4 years ago

Added a parameter under illumina conf to run ampliconstats (samtools development branch) if "--ampliconstats" flag is passed.

sb10 commented 4 years ago

Thanks @ac55-sanger . Unfortunately the tests are now failing for some reason that doesn't seem related to your changes? It's failing the installation of nextflow using conda.

Can you try and replicate this by running .github/scripts/install_conda.sh and then

export PATH=/opt/conda/bin:$PATH
conda install -c bioconda nextflow
NXF_VER=20.03.0-edge nextflow -version
m-bull commented 4 years ago

@sb10 - suggest installing Miniconda3 for tests: https://github.com/connor-lab/ncov2019-artic-nf/commit/319ca24d17d97acd7c74846e0c06e2471e09e166

ac55-sanger commented 4 years ago

@sb10 Followed the steps and it fails due to multiple conflicts.

@m-bull 's commit fixes it, just tested:

$NXF_VER=20.03.0-edge nextflow -version CAPSULE: Downloading dependency io.nextflow:nf-tower:jar:20.03.0-edge CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:20.03.0-edge CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:20.03.0-edge CAPSULE: Downloading dependency io.nextflow:nextflow:jar:20.03.0-edge CAPSULE: Downloading dependency jline:jline:jar:2.14.6 33 KB
N E X T F L O W version 20.03.0-edge build 5288 created 28-03-2020 11:10 UTC cite doi:10.1038/nbt.3820 http://nextflow.io

ac55-sanger commented 4 years ago

Added support to run ampliconstats on all the files in one got under: https://github.com/connor-lab/ncov2019-artic-nf/pull/58