From cdf0c5647404e9632913a4b4707864bcdebf6f0b Mon Sep 17 00:00:00 2001 From: Sarah Bastkowski Date: Sat, 28 Sep 2024 14:42:07 +0100 Subject: [PATCH] fix(plot): fixes a bug in the snakemake pipeline which uses the default mapping score of 30 when mapping score is set to 0 fixing dendropy dependency using latest 4.6 --- quatradis/pipelines/create_plots.smk | 2 +- requirements.txt | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/quatradis/pipelines/create_plots.smk b/quatradis/pipelines/create_plots.smk index 1091284..644e2fa 100644 --- a/quatradis/pipelines/create_plots.smk +++ b/quatradis/pipelines/create_plots.smk @@ -37,7 +37,7 @@ rule create_plot: aligner=("--aligner=" + config["aligner"]) if config["aligner"] else "", tag=("--tag=" + config["tag"]) if config["tag"] else "", mismatch=("--mismatch=" + str(config["mismatch"])) if config["mismatch"] else "", - mapping_score=("--mapping_score=" + str(config["mapping_score"])) if config["mapping_score"] else "", + mapping_score="--mapping_score=" + str(config["mapping_score"]), threads="--threads=" + str(config["threads"]) if config["threads"] else "", output_dir=os.path.join(config["output_dir"], "{fq}") threads: int(config["threads"]) diff --git a/requirements.txt b/requirements.txt index d36fa59..e8402cc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,11 +1,11 @@ pysam biopython cython -dendropy +dendropy==4.6 graphviz matplotlib numpy pandas scipy seaborn -snakeviz \ No newline at end of file +snakeviz