diff --git a/CHANGELOG.md b/CHANGELOG.md index 2cf29d5..ff49c77 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,9 +4,11 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [v0.3.15] - 2023-12-2023 +## [v0.3.15] - 2023-12-18 ### Added - `mini_align` can take a bam as input and optionally retain all or subset of bam tags. +### Changed +- Drop porechop dependency from pypi package due to blocking package uploads. Add warning to the user if porechop is called by `mini_assemble` but does not exist. ## [v0.3.14] - 2023-10-25 ### Changed diff --git a/requirements.txt b/requirements.txt index 4e10a3c..ec7d108 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,4 +7,3 @@ ncls numpy pandas pysam >= 0.15.4 -porechop @ git+https://github.com/artic-network/porechop diff --git a/scripts/mini_assemble b/scripts/mini_assemble index 09ee03c..5786bac 100755 --- a/scripts/mini_assemble +++ b/scripts/mini_assemble @@ -78,6 +78,14 @@ if $eflag && [[ $ERRCORR = *x ]]; then fi +if $CHOP && [[ ! $(command -v porechop) ]]; then + echo "-c requires porechop to be installed."; + echo "Run `pip install git+https://github.com/artic-network/porechop` or" + echo "`conda install -c bioconda artic-porechop`" + exit 1; +fi + + if $xflag; then set -x; fi