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Merge pull request #1 from icgc-argo-workflows/strelka2@0.1.0
Strelka2@0.1.0
2 parents e6715a7 + dea5b0c commit 1adfe2b

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‎strelka2/.dockerignore‎

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.gitignore
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.nextflow*
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tests
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work
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outdir

‎strelka2/Dockerfile‎

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FROM ubuntu:18.04
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LABEL org.opencontainers.image.source https://github.com/icgc-argo-workflows/argo-somatic-variant-calling
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ARG PYTHON_VERSION=2.7.5
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# Install dependencies
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# PIP - openssl version > 1.1 may be an issue (try older ubuntu images)
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RUN apt-get update \
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&& apt-get install -y wget gcc make openssl libffi-dev libgdbm-dev libsqlite3-dev libssl-dev zlib1g-dev \
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&& apt-get clean
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WORKDIR /tmp/
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# Build Python from source
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RUN wget https://www.python.org/ftp/python/$PYTHON_VERSION/Python-$PYTHON_VERSION.tgz \
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&& tar --extract -f Python-$PYTHON_VERSION.tgz \
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&& cd ./Python-$PYTHON_VERSION/ \
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&& ./configure --enable-optimizations --prefix=/usr/local \
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&& make && make install \
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&& cd ../ \
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&& rm -r ./Python-$PYTHON_VERSION*
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RUN apt-get install -y cmake g++ libboost-all-dev
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ARG STRELKA_VERSION=2.9.10
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RUN wget https://github.com/Illumina/strelka/releases/download/v${STRELKA_VERSION}/strelka-${STRELKA_VERSION}.release_src.tar.bz2 \
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&& tar -xjf strelka-${STRELKA_VERSION}.release_src.tar.bz2 \
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&& mkdir build && cd build \
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&& ../strelka-${STRELKA_VERSION}.release_src/configure --jobs=4 --prefix=/opt/strelka2 \
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&& make -j4 install \
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&& rm -fr /tmp/*
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ENV PATH="/tools:/opt/strelka2/bin:${PATH}"
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COPY *.py /tools/
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RUN groupadd -g 1000 ubuntu && \
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useradd -l -u 1000 -g ubuntu ubuntu && \
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install -d -m 0755 -o ubuntu -g ubuntu /home/ubuntu
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USER ubuntu
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WORKDIR /home/ubuntu
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ENTRYPOINT ["/usr/bin/env"]
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CMD ["/bin/bash"]

‎strelka2/main.nf‎

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#!/usr/bin/env nextflow
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/*
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Copyright (c) 2021, ICGC ARGO
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Authors:
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Junjun Zhang
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*/
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/********************************************************************/
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/* this block is auto-generated based on info from pkg.json where */
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/* changes can be made if needed, do NOT modify this block manually */
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nextflow.enable.dsl = 2
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version = '0.1.0' // package version
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/argo-somatic-variant-calling.strelka2'
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]
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default_container_registry = 'ghcr.io'
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/********************************************************************/
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// universal params go here
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params.container_registry = ""
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params.container_version = ""
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params.container = ""
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params.cpus = 1
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params.mem = 1 // GB
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params.publish_dir = "" // set to empty string will disable publishDir
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params.tumourBam = ""
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params.normalBam = ""
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params.referenceFa = ""
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params.isExome = false
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include { getSecondaryFiles as getSec } from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/helper-functions@1.0.2/main'
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process strelka2 {
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container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
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publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
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cpus params.cpus
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memory "${params.mem} GB"
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input:
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path tumourBam
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path tumourBai
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path normalBam
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path normalBai
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path referenceFa
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path referenceFai
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val isExome
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output:
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path "output_dir/results/variants/somatic.snvs.vcf.gz", emit: somaticSnvVcf
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path "output_dir/results/variants/somatic.snvs.vcf.gz.tbi", emit: somaticSnvVcfTbi
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path "output_dir/results/variants/somatic.indels.vcf.gz", emit: somaticIndelVcf
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path "output_dir/results/variants/somatic.indels.vcf.gz.tbi", emit: somaticIndelVcfTbi
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path "output_dir/results/stats/runStats.tsv", emit: runStats
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script:
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arg_exome = isExome == "true" ? "--exome" : ""
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"""
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mkdir -p output_dir
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configureStrelkaSomaticWorkflow.py \
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--tumorBam=${tumourBam} \
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--normalBam=${normalBam} \
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--referenceFasta=${referenceFa} \
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--callMemMb=${Math.round(params.mem * 1000 / params.cpus)} \
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--runDir=./output_dir ${arg_exome}
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./output_dir/runWorkflow.py -m local -j ${params.cpus}
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"""
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}
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// this provides an entry point for this main script, so it can be run directly without clone the repo
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// using this command: nextflow run <git_acc>/<repo>/<pkg_name>/<main_script>.nf -r <pkg_name>.v<pkg_version> --params-file xxx
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workflow {
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tumourIdx = params.tumourBam.endsWith('.bam') ? params.tumourBam + '.bai' : params.tumourBam + '.crai'
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normalIdx = params.normalBam.endsWith('.bam') ? params.normalBam + '.bai' : params.normalBam + '.crai'
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referenceIdx = params.referenceFa.endsWith('.fa.gz') ? getSec(params.referenceFa, ['fai', 'gzi']) : getSec(params.referenceFa, ['fai'])
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strelka2(
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file(params.tumourBam),
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file(tumourIdx),
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file(params.normalBam),
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file(normalIdx),
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file(params.referenceFa),
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Channel.fromPath(referenceIdx, checkIfExists: true).collect(),
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params.isExome
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)
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}

‎strelka2/nextflow.config‎

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docker {
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enabled = true
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runOptions = '-u \$(id -u):\$(id -g)'
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}

‎strelka2/pkg.json‎

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{
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"name": "strelka2",
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"version": "0.1.0",
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"description": "Strelka2 Small Variant Caller",
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"main": "main.nf",
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"deprecated": false,
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"keywords": [
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"bioinformatics",
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"genomics",
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"variant caller",
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"ngs"
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],
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"repository": {
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"type": "git",
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"url": "https://github.com/icgc-argo-workflows/argo-somatic-variant-calling.git"
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},
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"container": {
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"registries": [
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{
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"registry": "ghcr.io",
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"type": "docker",
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"org": "icgc-argo-workflows",
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"default": true
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}
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]
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},
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"dependencies": [
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"github.com/icgc-argo-workflows/data-processing-utility-tools/helper-functions@1.0.2"
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],
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"devDependencies": [],
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"contributors": [
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{
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"name": "Junjun Zhang",
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"email": "junjun.ca@gmail.com"
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}
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],
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"license": "MIT",
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"bugReport": "https://github.com/icgc-argo-workflows/argo-somatic-variant-calling/issues",
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"homepage": "https://github.com/icgc-argo-workflows/argo-somatic-variant-calling#readme"
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}

‎strelka2/tests/checker.nf‎

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#!/usr/bin/env nextflow
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/*
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Copyright (c) 2021, ICGC ARGO
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Authors:
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Junjun Zhang
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*/
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/*
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This is an auto-generated checker workflow to test the generated main template workflow, it's
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meant to illustrate how testing works. Please update to suit your own needs.
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*/
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/********************************************************************/
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/* this block is auto-generated based on info from pkg.json where */
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/* changes can be made if needed, do NOT modify this block manually */
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nextflow.enable.dsl = 2
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version = '0.1.0' // package version
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/argo-somatic-variant-calling.strelka2'
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]
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default_container_registry = 'ghcr.io'
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/********************************************************************/
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// universal params
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params.container_registry = ""
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params.container_version = ""
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params.container = ""
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// tool specific parmas go here, add / change as needed
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params.tumourBam = ""
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params.normalBam = ""
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params.referenceFa = ""
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params.isExome = true
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params.expected_snv_output = ""
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params.expected_indel_output = ""
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include { strelka2 } from '../main'
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include { getSecondaryFiles as getSec } from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/helper-functions@1.0.2/main'
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process file_smart_diff {
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container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
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input:
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path output_somaticSnvVcf
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path expected_snv_output
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path output_somaticIndelVcf
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path expected_indel_output
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output:
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stdout()
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script:
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"""
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gunzip -c ${output_somaticSnvVcf} \
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| grep -v '^#' > normalized_output_somaticSnvVcf
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gunzip -c ${expected_snv_output} \
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| grep -v '^#' > normalized_expected_snv_output
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diff normalized_output_somaticSnvVcf normalized_expected_snv_output \
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&& ( echo -n "SNV calls MATCH. " ) || ( echo "Test FAILED, output SNV calls mismatch." && exit 1 )
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gunzip -c ${output_somaticIndelVcf} \
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| grep -v '^#' > normalized_output_somaticIndelVcf
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gunzip -c ${expected_indel_output} \
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| grep -v '^#' > normalized_expected_indel_output
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diff normalized_output_somaticIndelVcf normalized_expected_indel_output \
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&& ( echo "Indel calls MATCH. Test PASSED" && exit 0 ) || ( echo "Test FAILED, output Indel calls mismatch." && exit 1 )
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"""
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}
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workflow checker {
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take:
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tumourBam
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tumourBai
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normalBam
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normalBai
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referenceFa
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referenceFai
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isExome
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expected_snv_output
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expected_indel_output
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main:
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strelka2(
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tumourBam,
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tumourBai,
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normalBam,
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normalBai,
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referenceFa,
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referenceFai,
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isExome
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)
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file_smart_diff(
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strelka2.out.somaticSnvVcf,
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expected_snv_output,
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strelka2.out.somaticIndelVcf,
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expected_indel_output
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)
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}
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workflow {
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tumourIdx = params.tumourBam.endsWith('.bam') ? params.tumourBam + '.bai' : params.tumourBam + '.crai'
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normalIdx = params.normalBam.endsWith('.bam') ? params.normalBam + '.bai' : params.normalBam + '.crai'
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referenceIdx = params.referenceFa.endsWith('.fa.gz') ? getSec(params.referenceFa, ['fai', 'gzi']) : getSec(params.referenceFa, ['fai'])
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checker(
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file(params.tumourBam),
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file(tumourIdx),
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file(params.normalBam),
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file(normalIdx),
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file(params.referenceFa),
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Channel.fromPath(referenceIdx, checkIfExists: true).collect(),
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params.isExome,
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file(params.expected_snv_output),
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file(params.expected_indel_output)
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)
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}

‎strelka2/tests/expected/expected.somatic.indels.vcf.gz‎

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‎strelka2/tests/expected/expected.somatic.snvs.vcf.gz‎

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‎strelka2/tests/input/NA12891_demo20.bam‎

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‎strelka2/tests/input/NA12891_demo20.bam.bai‎

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