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Release 0.9.3 (#83)
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‎Dockerfile‎

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## build env ##
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FROM ubuntu:24.04 AS build
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# get necessary libs
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RUN apt-get update && \
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apt install -y make wget gcc bzip2 libz-dev libbz2-dev liblzma-dev libcurl4-openssl-dev build-essential python3-dev pip libtool cmake git zlib1g-dev openjdk-11-jdk bash
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# samtools
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RUN wget -O- "https://github.com/samtools/samtools/releases/download/1.21/samtools-1.21.tar.bz2" | tar -xj && \
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cd samtools-* && \
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./configure --without-curses && \
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make && \
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make install
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# htslib
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RUN wget -O- "https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2" | tar -xj && \
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cd htslib-* && \
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./configure && \
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make && \
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make install
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# minimap2
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RUN wget -O- "https://github.com/lh3/minimap2/archive/refs/tags/v2.28.tar.gz" | tar -zx && \
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cd minimap2-* && \
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make && \
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chmod a+x minimap2 && \
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mv minimap2 /usr/local/bin/
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# mosdepth
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RUN wget "https://github.com/brentp/mosdepth/releases/download/v0.3.9/mosdepth" && \
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chmod a+x mosdepth && \
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mv mosdepth /usr/local/bin/
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# bcftools
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RUN wget -O- "https://github.com/samtools/bcftools/releases/download/1.21/bcftools-1.21.tar.bz2" | tar -xj && \
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cd bcftools-* && \
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make && \
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make install && \
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mkdir -p /usr/local/libexec/bcftools/ && \
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mv /bcftools-1.21/plugins/* /usr/local/libexec/bcftools/
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# whatshap
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RUN pip install whatshap==2.3 --break-system-packages
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# minimod
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RUN wget -O- "https://github.com/warp9seq/minimod/releases/download/v0.3.0/minimod-v0.3.0-release.tar.gz" | tar -xz && \
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cd minimod-* && \
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./scripts/install-hts.sh && \
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make && \
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mv minimod /usr/local/bin/
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# kentutils (bedGraphToBigWig only)
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RUN wget "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig" && \
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chmod a+x bedGraphToBigWig && \
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mv bedGraphToBigWig /usr/local/bin/
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# cutesv
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RUN pip install cuteSV==2.1.1 --break-system-packages
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# sniffles
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RUN pip install sniffles==2.6.0 --break-system-packages
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# somalier
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RUN wget "https://github.com/brentp/somalier/releases/download/v0.2.19/somalier" && \
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chmod a+x somalier && \
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mv somalier /usr/local/bin/
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# spectre
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RUN pip install spectre-cnv==0.2.1 --break-system-packages
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# snf2json
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RUN pip install snf2json==0.1.0 --break-system-packages
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# bedtools
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RUN wget "https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static" && \
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chmod a+x bedtools.static && \
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mv bedtools.static /usr/local/bin/bedtools
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# racon
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RUN git clone --recursive https://github.com/lbcb-sci/racon.git racon && \
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cd racon && \
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git checkout tags/1.4.3 && \
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git submodule update --init --recursive && \
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mkdir build && \
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cd build && \
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cmake -DCMAKE_BUILD_TYPE=Release .. && \
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make
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# jasmine
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RUN git clone --recurse-submodules https://github.com/bioinfomethods/Jasmine.git && \
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cd Jasmine && \
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git checkout tags/1.1.5-r1 && \
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./build_jar.sh && \
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sed -i '1s|^.*$|#!/bin/bash|' jasmine
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## deploy env ##
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FROM ubuntu:24.04 AS deploy
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LABEL name="pipeface"
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LABEL description="docker image containing most software required for pipeface"
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LABEL version="0.0.1"
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LABEL maintainer.name="Leah Kemp"
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LABEL maintainer.email="leahmhkemp@gmail.com"
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# get necessary libs
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RUN apt-get update && \
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apt install -y python3-dev libcurl4-openssl-dev openjdk-11-jdk
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# copy required compiled tools
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COPY --from=build \
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/usr/local/bin/samtools \
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/usr/local/bin/bgzip \
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/usr/local/bin/tabix \
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/usr/local/bin/minimap2 \
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/usr/local/bin/mosdepth \
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/usr/local/bin/bcftools \
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/usr/local/bin/whatshap \
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/usr/local/bin/minimod \
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/usr/local/bin/bedGraphToBigWig \
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/usr/local/bin/cuteSV \
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/usr/local/bin/sniffles \
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/usr/local/bin/somalier \
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/usr/local/bin/spectre \
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/usr/local/bin/snf2json \
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/usr/local/bin/bedtools \
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/racon/build/bin/racon \
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/Jasmine/jasmine \
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/Jasmine/jasmine.jar \
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/Jasmine/jasmine_iris.jar \
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/usr/local/bin/
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COPY --from=build \
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/usr/local/libexec/bcftools/* \
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/usr/local/libexec/bcftools/
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COPY --from=build \
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/usr/local/lib/ \
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/usr/local/lib/
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‎README.md‎

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- [minimod](https://github.com/warp9seq/minimod?tab=readme-ov-file)
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- [ensembl-vep](https://github.com/Ensembl/ensembl-vep)
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*[See the list of software and their versions used by this version of pipeface](./docs/software_versions.txt) as well as the [list of variant databases and their versions](./docs/database_versions.txt) if variant annotation is carried out (assuming the default [nextflow_pipeface.config](./config/nextflow_pipeface.config) file is used).*
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## Main input files
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### Required
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- Enables correct handling of the haploid nature of chrX and chrY for XY samples, along with PAR regions
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- Only supported for singletons at the moment
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## Assumptions
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- Running pipeline on Australia's [National Computational Infrastructure (NCI)](https://nci.org.au/)
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- Access to if89 project (to access software installs used by pipeface)
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- Access to xy86 project (to access variant databases used by pipeface, only required if running variant annotation)
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*[See the list of software and their versions used by this version of pipeface](./docs/software_versions.txt) as well as the [list of variant databases and their versions](./docs/database_versions.txt) if variant annotation is carried out (assuming the default [nextflow_pipeface.config](./config/nextflow_pipeface.config) file is used).*
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## Run it!
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See a walkthrough for [running pipeface on NCI](./docs/run_on_nci.md).
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See a walkthrough for [setting up](./docs/setup.md) and [running pipeface on NCI](./docs/run_on_nci.md) or [another HPC](./docs/run_on_other_hpc.md).
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## Credit
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‎config/nextflow_pipeface.config‎

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module = 'mosdepth/0.3.9'
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}
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withName: 'clair3' {
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withName: 'clair3|clair3_haploid_aware' {
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queue = 'normal'
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cpus = '32'
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memory = '128GB'
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disk = '20GB'
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time = '16h'
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module = 'bedtools/2.31.0:bcftools/1.21:htslib/1.20:clair3/v1.0.9'
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module = 'clair3/v1.0.9'
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}
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withName: 'clair3_pre_processing|clair3_post_processing' {
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queue = 'normal'
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cpus = '1'
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memory = '4GB'
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time = '30m'
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module = 'bedtools/2.31.0'
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}
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withName: 'clair3_post_processing' {
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queue = 'normal'
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cpus = '1'
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memory = '4GB'
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disk = '10GB'
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time = '30m'
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module = 'bcftools/1.21:htslib/1.20'
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beforeScript = 'module use -a /g/data/if89/apps/modulefiles && module use -a /g/data/if89/shpcroot/modules && BCFTOOLS_PLUGINS=/apps/bcftools/1.12/libexec/bcftools'
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}
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memory = '128GB'
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disk = '10GB'
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time = '1h'
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module = 'deepvariant-gpu/1.8.0:bcftools/1.21:htslib/1.20'
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module = 'deepvariant-gpu/1.8.0'
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}
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withName: 'filter_ref_call' {
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queue = 'normal'
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cpus = '1'
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memory = '4GB'
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time = '1h'
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module = 'bcftools/1.21'
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}
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withName: 'split_multiallele|split_multiallele_duo|split_multiallele_trio' {
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cpus = '1'
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module = 'glnexus/1.4.3:bcftools/1.21:htslib/1.20'
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module = 'glnexus/1.4.3'
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}
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withName: 'glnexus_post_processing_duo|glnexus_post_processing_trio' {
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queue = 'normal'
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cpus = '1'
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memory = '4GB'
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time = '30m'
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module = 'bcftools/1.21:htslib/1.20'
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}
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withName: 'sniffles' {

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