diff --git a/PARANOiD.nf b/PARANOiD.nf index f437072..2dcb058 100644 --- a/PARANOiD.nf +++ b/PARANOiD.nf @@ -358,7 +358,7 @@ process deduplicate{ file "${query.baseName}.deduplicated.log*" into log_deduplicate_to_collect_statistics """ - umi_tools dedup -I ${query} --output-stats ${query.baseName}.deduplicated.log -S ${query.baseName}.deduplicated.bam + umi_tools dedup --random-seed=42 -I ${query} --output-stats ${query.baseName}.deduplicated.log -S ${query.baseName}.deduplicated.bam """ } diff --git a/dockerfiles/dockerfile.umi-tools b/dockerfiles/dockerfile.umi-tools index 5973469..5a71e60 100644 --- a/dockerfiles/dockerfile.umi-tools +++ b/dockerfiles/dockerfile.umi-tools @@ -6,8 +6,16 @@ LABEL tool.version="1.1.2" MAINTAINER Patrick Barth RUN apt-get update -y && \ - apt-get install -y gcc procps && \ - pip install umi-tools==1.1.2 && \ - apt-get purge -y gcc && \ + apt-get install -y gcc procps patch wget && \ + wget -q https://github.com/CGATOxford/UMI-tools/archive/refs/tags/1.1.2.tar.gz && \ + tar xzf 1.1.2.tar.gz && \ + cd UMI-tools-1.1.2 && \ + wget -q -O - https://patch-diff.githubusercontent.com/raw/CGATOxford/UMI-tools/pull/550.diff | patch -p1 && \ + python setup.py install && \ + cd .. && \ + rm -rf UMI-tools-1.1.2 1.1.2.tar.gz && \ + apt-get purge -y gcc patch wget && \ apt-get -y autoremove +CMD ["umi_tools"] +