Merge pull request #108 from Pathogen-Genomics-Cymru/bcg

Bcg

Author: t-whalley

.github/workflows/build-push-quay.yml

@@ -3,7 +3,7 @@ on:
   push:
     branches:
       - main
-      - ntmprofiler
+      - bcg
     paths:
       - '**/Dockerfile*'
       - "bin/"

README.md

@@ -2,7 +2,20 @@
 ![Build Status](https://github.com/Pathogen-Genomics-Cymru/lodestone/workflows/build-push-quay/badge.svg)
 ![Build Status](https://github.com/Pathogen-Genomics-Cymru/lodestone/workflows/pytest/badge.svg)
 ![Build Status](https://github.com/Pathogen-Genomics-Cymru/lodestone/workflows/stub-run/badge.svg)
-  
+
+## Table of Contents
+- [What is Lodestone](#what-is-lodestone)
+- [Quick Start](#quick-start)
+- [Executors](#executors)
+- [System Requirements](#system-requirements)
+- [Parameters](#parameters)
+- [Stub Runs](#stub-runs)
+- [Checkpoints](#checkpoints)
+- [Acknowledgments](#acknowledgements)
+- [License](#-license)
+
+## What is Lodestone?
+ 
 This pipeline takes as input reads presumed to be from one of 10 mycobacterial genomes: abscessus, africanum, avium, bovis, chelonae, chimaera, fortuitum, intracellulare, kansasii, tuberculosis. Input should be in the form of one directory containing pairs of fastq(.gz) or bam files.
 
 Pipeline cleans and QCs reads with fastp and FastQC, classifies with Kraken2 & Afanc, removes non-bacterial content, and - by alignment to any minority genomes - disambiguates mixtures of bacterial reads. Cleaned reads are aligned to either of the 10 supported genomes and variants called. Produces as output one directory per sample, containing cleaned fastqs, sorted, indexed BAM, VCF, F2 and F47 statistics, an antibiogram and summary reports.
@@ -40,7 +53,7 @@ By default, the pipeline will just run on the local machine. To run on a cluster
 ### System Requirements ###
 Minimum recommended requirements: 32GB RAM, 8CPU
 
-## Params ##
+## Paramaters ##
 The following parameters should be set in `nextflow.config` or specified on the command line:
 
 * **input_dir**<br /> 
@@ -84,7 +97,7 @@ For more information on the parameters run `nextflow run main.nf --help`
 
 The path to the singularity images can also be changed in the singularity profile in `nextflow.config`. Default value is `${baseDir}/singularity`
 
-## Stub-run ##
+## Stub runs ##
 To test the stub run:
 ```
 NXF_VER=20.11.0-edge nextflow run main.nf -stub -config testing.config
@@ -150,3 +163,5 @@ For a list of direct authors of this pipeline, please see the contributors list.
 
 The preprocessing sub-workflow is based on the preprocessing nextflow DSL1 pipeline written by Stephen Bush, University of Oxford. The clockwork sub-workflow uses aspects of the variant calling workflow from https://github.com/iqbal-lab-org/clockwork, lead author Martin Hunt, Iqbal Lab at EMBL-EBI
 
+## License
+The tool is licensed under the V3 GNU Affero GPL license. Please see the [LICENSE](LICENSE) file for more details.

bin/identify_tophit_and_contaminants2.py

@@ -359,8 +359,21 @@ def process_reports(afanc_json_path, kraken_json_path, supposed_species, unmix_m
 
     # IS THE TOP SPECIES HIT ONE OF THE 10 ACCEPTABLE POSSIBILITIES? IF SO, PROVIDE A LINK TO THE REFERENCE GENOME
     re_top_species = re.findall(r"^(Mycobact|Mycolicibac)\w+ (abscessus|africanum|avium|bovis|chelonae|chimaera|fortuitum|intracellulare|kansasii|tuberculosis).*?$", top_species)
+    re_top_variant = re.findall(r"^(Mycobact|Mycolicibac)\w+ (abscessus|africanum|avium|bovis|chelonae|chimaera|fortuitum|intracellulare|kansasii|tuberculosis) ()\w+ (bovis|orgis|caprae).*?$", top_species)
+    if len(re_top_variant) != 0:
+        re_top_species = re_top_variant
     if len(re_top_species) > 0:
-        identified_species = re_top_species[0][1]
+        if len(re_top_species[0]) == 2:
+            identified_species = re_top_species[0][1]
+            #deal with lineages
+            lineage_dict = {"La1.": "bovis",
+                            "La2.": "caprae",
+                            "La3.": "orygis"}
+            for lineage in lineage_dict:
+                if lineage in top_species:
+                    identified_species = lineage_dict[lineage]
+        else:
+            identified_species = re_top_species[0][3] #we have bovis (or  orgis/caprae) with variant in the name
         if supposed_species == 'null':
             out['summary_questions']['is_the_top_species_appropriate'] = 'yes'
         elif ((supposed_species != 'null') & (supposed_species == identified_species)):

bin/run-vcfmix.py

@@ -9,10 +9,10 @@
 
 def go(vcf_file):
     # create a lineagescan object
-    v = lineageScan()
+    v = lineageScan(minos=True)
 
-    # assuming postfix of ".bcftools.vcf"
-    sampleid = vcf_file[:-13]
+    # assuming postfix of ".minos.vcf"
+    sampleid = vcf_file.replace("_allelic_depth.minos.vcf", "")
     print(sampleid)
 
     res = v.parse(vcffile=vcf_file, sample_id=sampleid)

config/containers.config

@@ -33,10 +33,10 @@ process {
     }
 
     withLabel:clockwork {
-        container = "quay.io/pathogen-genomics-cymru/clockwork:0.9.9"
+        container = "quay.io/pathogen-genomics-cymru/clockwork:0.9.9r1"
     }
 
     withLabel:vcfpredict {
-        container = "quay.io/pathogen-genomics-cymru/vcfpredict:0.9.9"
+        container = "quay.io/pathogen-genomics-cymru/vcfpredict:0.9.9r1"
     }
  }

docker/Dockerfile.clockwork-0.9.9

@@ -1,4 +1,5 @@
-FROM debian:buster
+FROM ubuntu:focal
+
 
 LABEL maintainer="[email protected]" \
 about.summary="container for the clockwork workflow"
@@ -16,17 +17,17 @@ vcftools_version=0.1.15 \
 mccortex_version=97aba198d632ee98ac1aa496db33d1a7a8cb7e51 \
 stampy_version=1.0.32r3761 \
 python_version=3.6.5 \
-clockwork_version=2364dec4cbf25c844575e19e8fe0a319d10721b5
+clockwork_version=2364dec4cbf25c844575e19e8fe0a319d10721b5 \
+gatk_version=4.6.0.0
 
 ENV PACKAGES="procps curl git build-essential wget zlib1g-dev pkg-config jq r-base-core rsync autoconf libncurses-dev libbz2-dev liblzma-dev libcurl4-openssl-dev cmake tabix libvcflib-tools libssl-dev software-properties-common perl locales locales-all" \
 PYTHON="python2.7 python-dev"
 
 COPY bin/ /opt/bin/
 ENV PATH=/opt/bin:$PATH
 
-
 RUN apt-get update \
-&& apt-get install -y $PACKAGES $PYTHON \
+&& DEBIAN_FRONTEND=noninteractive apt-get install -y $PACKAGES $PYTHON \
 && curl -fsSL https://www.python.org/ftp/python/${python_version}/Python-${python_version}.tgz | tar -xz \
 && cd Python-${python_version} \
 && ./configure --enable-optimizations \
@@ -36,7 +37,15 @@ RUN apt-get update \
 && ln -s /usr/local/bin/pip3.6 /usr/local/bin/pip3 \
 && pip3 install --upgrade pip \
 && pip3 install 'cluster_vcf_records==0.13.1' pysam setuptools  awscli \
-&& apt-get update && apt-get install -y openjdk-11-jdk
+&& apt-get update
+
+#update jdk
+RUN wget https://download.java.net/java/GA/jdk18/43f95e8614114aeaa8e8a5fcf20a682d/36/GPL/openjdk-18_linux-x64_bin.tar.gz
+RUN tar -xvf openjdk-18_linux-x64_bin.tar.gz
+RUN mv jdk-18* /opt/
+ENV JAVA_HOME=/opt/jdk-18
+ENV PATH=$PATH:$JAVA_HOME/bin
+
 
 RUN curl -fsSL https://github.com/samtools/samtools/archive/${samtools_version}.tar.gz | tar -xz \
 && curl -fsSL https://github.com/samtools/htslib/releases/download/${htslib_version}/htslib-${htslib_version}.tar.bz2 | tar -xj \
@@ -107,8 +116,12 @@ RUN git clone --recursive https://github.com/iqbal-lab/cortex.git \
 && pip3 install . \
 && chmod +x scripts/clockwork
 
+RUN wget https://github.com/broadinstitute/gatk/releases/download/${gatk_version}/gatk-${gatk_version}.zip -O /tmp/gatk-${gatk_version}.zip\
+	&& unzip /tmp/gatk-${gatk_version}.zip -d /opt/ \
+	&& rm /tmp/gatk-${gatk_version}.zip -f
+
 ENV CLOCKWORK_CORTEX_DIR=/cortex \
-PATH=${PATH}:/clockwork/python/scripts \
+PATH=${PATH}:/clockwork/python/scripts:/opt/gatk-${gatk_version} \
 PICARD_JAR=/usr/local/bin/picard.jar
 
 ENV LC_ALL en_US.UTF-8 \

docker/Dockerfile.clockwork-0.9.9r1

@@ -0,0 +1,131 @@
+FROM ubuntu:focal
+
+
+LABEL maintainer="[email protected]" \
+about.summary="container for the clockwork workflow"
+
+ENV samtools_version=1.12 \
+htslib_version=1.12 \
+bcftools_version=1.12 \
+minimap2_version=2.17 \
+picard_version=2.18.16 \
+gramtools_version=8af53f6c8c0d72ef95223e89ab82119b717044f2 \
+vt_version=2187ff6347086e38f71bd9f8ca622cd7dcfbb40c \
+minos_version=0.11.0 \
+cortex_version=3a235272e4e0121be64527f01e73f9e066d378d3 \
+vcftools_version=0.1.15 \
+mccortex_version=97aba198d632ee98ac1aa496db33d1a7a8cb7e51 \
+stampy_version=1.0.32r3761 \
+python_version=3.6.5 \
+clockwork_version=2364dec4cbf25c844575e19e8fe0a319d10721b5 \
+gatk_version=4.6.0.0
+
+ENV PACKAGES="procps curl git build-essential wget zlib1g-dev pkg-config jq r-base-core rsync autoconf libncurses-dev libbz2-dev liblzma-dev libcurl4-openssl-dev cmake tabix libvcflib-tools libssl-dev software-properties-common perl locales locales-all" \
+PYTHON="python2.7 python-dev"
+
+COPY bin/ /opt/bin/
+ENV PATH=/opt/bin:$PATH
+
+RUN apt-get update \
+&& DEBIAN_FRONTEND=noninteractive apt-get install -y $PACKAGES $PYTHON \
+&& curl -fsSL https://www.python.org/ftp/python/${python_version}/Python-${python_version}.tgz | tar -xz \
+&& cd Python-${python_version} \
+&& ./configure --enable-optimizations \
+&& make altinstall \
+&& cd .. \
+&& ln -s /usr/local/bin/python3.6 /usr/local/bin/python3 \
+&& ln -s /usr/local/bin/pip3.6 /usr/local/bin/pip3 \
+&& pip3 install --upgrade pip \
+&& pip3 install 'cluster_vcf_records==0.13.1' pysam setuptools  awscli \
+&& apt-get update
+
+#update jdk
+RUN wget https://download.java.net/java/GA/jdk18/43f95e8614114aeaa8e8a5fcf20a682d/36/GPL/openjdk-18_linux-x64_bin.tar.gz
+RUN tar -xvf openjdk-18_linux-x64_bin.tar.gz
+RUN mv jdk-18* /opt/
+ENV JAVA_HOME=/opt/jdk-18
+ENV PATH=$PATH:$JAVA_HOME/bin
+
+
+RUN curl -fsSL https://github.com/samtools/samtools/archive/${samtools_version}.tar.gz | tar -xz \
+&& curl -fsSL https://github.com/samtools/htslib/releases/download/${htslib_version}/htslib-${htslib_version}.tar.bz2 | tar -xj \
+&& make -C samtools-${samtools_version} -j HTSDIR=../htslib-${htslib_version} \
+&& make -C samtools-${samtools_version} -j HTSDIR=../htslib-${htslib_version} prefix=/usr/local install \
+&& rm -r samtools-${samtools_version} \
+&& curl -fsSL https://github.com/samtools/bcftools/archive/refs/tags/${bcftools_version}.tar.gz | tar -xz \
+&& make -C bcftools-${bcftools_version} -j HTSDIR=../htslib-${htslib_version} \
+&& make -C bcftools-${bcftools_version} -j HTSDIR=../htslib-${htslib_version} prefix=/usr/local install \
+&& rm -r bcftools-${bcftools_version}
+
+
+RUN curl -fsSL minimap2-${minimap2_version}.tar.gz https://github.com/lh3/minimap2/archive/v${minimap2_version}.tar.gz | tar -xz \
+&& cd minimap2-${minimap2_version} \
+&& make \
+&& chmod +x minimap2 \
+&& mv minimap2 /usr/local/bin \
+&& cd .. \
+&& rm -r minimap2-${minimap2_version} \
+&& wget https://github.com/broadinstitute/picard/releases/download/${picard_version}/picard.jar -O /usr/local/bin/picard.jar
+
+
+RUN git clone https://github.com/atks/vt.git vt-git \
+&& cd vt-git \
+&& git checkout ${vt_version} \
+&& make \
+&& cd .. \
+&& mv vt-git/vt /usr/local/bin \
+&& pip3 install tox "six>=1.14.0" \
+&& git clone https://github.com/iqbal-lab-org/gramtools \
+&& cd gramtools \
+&& git checkout ${gramtools_version} \
+&& pip3 install . \
+&& cd .. \
+&& pip3 install cython \
+&& pip3 install git+https://github.com/iqbal-lab-org/minos@v${minos_version}
+
+
+RUN git clone --recursive https://github.com/iqbal-lab/cortex.git \
+&& cd cortex \
+&& git checkout ${cortex_version} \
+&& bash install.sh \
+&& make NUM_COLS=1 cortex_var \
+&& make NUM_COLS=2 cortex_var \
+&& cd .. \
+&& mkdir bioinf-tools \
+&& cd bioinf-tools \
+&& curl -fsSL http://www.well.ox.ac.uk/~gerton/software/Stampy/stampy-${stampy_version}.tgz | tar -xz \
+&& make -C stampy-* \
+&& cp -s stampy-*/stampy.py . \
+&& curl -fsSL https://github.com/vcftools/vcftools/releases/download/v${vcftools_version}/vcftools-${vcftools_version}.tar.gz | tar -xz \
+&& cd vcftools-${vcftools_version} \
+&& ./configure --prefix $PWD/install \
+&& make && make install \
+&& ln -s src/perl/ . \
+&& cd .. \
+&& git clone --recursive https://github.com/mcveanlab/mccortex \
+&& cd mccortex \
+&& git checkout ${mccortex_version} \
+&& make all \
+&& cd .. \
+&& cp -s mccortex/bin/mccortex31 . \
+&& cd .. \
+&& git clone https://github.com/iqbal-lab-org/clockwork \
+&& cd clockwork \
+&& git checkout ${clockwork_version} \
+&& cd python \
+&& pip3 install . \
+&& chmod +x scripts/clockwork
+
+RUN wget https://github.com/broadinstitute/gatk/releases/download/${gatk_version}/gatk-${gatk_version}.zip -O /tmp/gatk-${gatk_version}.zip\
+	&& unzip /tmp/gatk-${gatk_version}.zip -d /opt/ \
+	&& rm /tmp/gatk-${gatk_version}.zip -f
+
+ENV CLOCKWORK_CORTEX_DIR=/cortex \
+PATH=${PATH}:/clockwork/python/scripts:/opt/gatk-${gatk_version} \
+PICARD_JAR=/usr/local/bin/picard.jar
+
+ENV LC_ALL en_US.UTF-8 \
+LANG en_US.UTF-8 \
+LANGUAGE en_US.UTF-8
+
+

docker/Dockerfile.tbprofiler-0.9.9

@@ -42,8 +42,7 @@ RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest| tar -xvj bin
 # install tb-profiler via bioconda; install into 'base' conda env
 RUN micromamba install --yes --name base --channel conda-forge --channel bioconda  \
     tb-profiler=${TBPROFILER_VER}
-
-RUN micromamba install --yes --name base --channel conda-forge --channel bioconda gatk4 
+RUN micromamba install --yes --name base --channel conda-forge --channel bioconda gatk4
 RUN micromamba install --yes --name base --channel conda-forge --channel bioconda samtools 
 RUN micromamba install --yes --name base --channel conda-forge jq
 RUN micromamba clean --all --yes

docker/Dockerfile.tbtamr-0.9.9

@@ -2,6 +2,9 @@ FROM ubuntu:jammy
 
 WORKDIR /
 
+ENV freebayes_version=1.3.6 \
+    tbtamr_version=0.0.4
+
 # LABEL instructions tag the image with metadata that might be important to the user
 LABEL base.image="ubuntu:jammy"
 LABEL dockerfile.version="0.9.9"

docker/Dockerfile.vcfpredict-0.9.9r1

@@ -0,0 +1,26 @@
+FROM ubuntu:20.04
+
+LABEL maintainer="[email protected]" \
+about.summary="container for the vcf predict workflow"
+
+#add run-vcf to container
+COPY bin/ /opt/bin/
+ENV PATH=/opt/bin:$PATH
+
+ENV PACKAGES="procps curl wget git build-essential libhdf5-dev libffi-dev r-base-core jq" \
+PYTHON="python3 python3-pip python3-dev"
+
+ENV vcfmix_version=d4693344bf612780723e39ce27c8ae3868f95417
+
+#apt updates
+RUN apt-get update \
+&& DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata \
+&& apt-get install -y $PACKAGES $PYTHON \
+&& apt-get install -y python3-packaging \
+&& git clone https://github.com/whalleyt/VCFMIX.git \
+&& cd VCFMIX \
+&& pip3 install recursive_diff \
+&& pip3 install awscli \
+&& pip3 install . \
+&& cp -r data /usr/local/lib/python3.8/dist-packages \
+&& cd ..