diff --git a/docker/Dockerfile.clockwork-0.9.8 b/docker/Dockerfile.clockwork-0.9.8
deleted file mode 100644
index fce2997..0000000
--- a/docker/Dockerfile.clockwork-0.9.8
+++ /dev/null
@@ -1,119 +0,0 @@
-FROM debian:buster
-
-LABEL maintainer="pricea35@cardiff.ac.uk" \
-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
-
-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 $PYTHON \
-&& curl -fsSL https://www.python.org/ftp/python/${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 && apt-get install -y openjdk-11-jdk
-
-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 ${clockwork_version} \
-&& cd python \
-&& pip3 install . \
-&& chmod +x scripts/clockwork
-
-ENV CLOCKWORK_CORTEX_DIR=/cortex \
-PATH=${PATH}:/clockwork/python/scripts \
-PICARD_JAR=/usr/local/bin/picard.jar
-
-ENV LC_ALL en_US.UTF-8 \
-LANG en_US.UTF-8 \
-LANGUAGE en_US.UTF-8
-
-
diff --git a/docker/Dockerfile.preprocessing-0.9.8.1 b/docker/Dockerfile.preprocessing-0.9.8.1
deleted file mode 100644
index 0c4da95..0000000
--- a/docker/Dockerfile.preprocessing-0.9.8.1
+++ /dev/null
@@ -1,132 +0,0 @@
-FROM ubuntu:focal
-
-LABEL maintainer="pricea35@cardiff.ac.uk" \
-about.summary="container for the preprocessing workflow"
-
-ENV samtools_version=1.12 \
-bcftools_version=1.12 \
-htslib_version=1.12 \
-bedtools_version=2.29.2 \
-bowtie2_version=2.4.2 \
-fastp_version=0.20.1 \
-fastqc_version=0.11.9 \
-fqtools_version=2.3 \
-kraken2_version=2.1.1 \
-afanc_version=0.10.2 \
-mykrobe_version=0.12.1 \
-bwa_version=0.7.17 \
-mash_version=2.3 \
-fastani_version=1.33
-
-
-ENV PACKAGES="procps curl git wget build-essential zlib1g-dev libncurses-dev libz-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libgsl-dev rsync unzip ncbi-blast+ pigz jq libtbb-dev openjdk-11-jre-headless autoconf r-base-core locales locales-all" \
-PYTHON="python3 python3-pip python3-dev" \
-PYTHON_PACKAGES="biopython awscli boto3"
-
-ENV PATH=${PATH}:/usr/local/bin/mccortex/bin:/usr/local/bin/bwa-${bwa_version}:/opt/edirect \
-LD_LIBRARY_PATH=/usr/local/lib
-
-RUN export DEBIAN_FRONTEND="noninteractive"
-
-COPY bin/ /opt/bin/
-ENV PATH=/opt/bin:$PATH
-
-RUN apt-get update \
-&& DEBIAN_FRONTEND="noninteractive" apt-get install -y $PACKAGES $PYTHON \
-&& pip3 install --upgrade pip \
-&& pip3 install $PYTHON_PACKAGES \
-&& ln -s /usr/bin/python3 /usr/bin/python
-
-RUN curl -fsSL https://github.com/samtools/samtools/archive/${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-${bcftools_version}
-
-RUN curl -fsSL https://github.com/alastair-droop/fqtools/archive/v${fqtools_version}.tar.gz | tar -xz \
-&& mv htslib-${htslib_version} fqtools-${fqtools_version} \
-&& cd fqtools-${fqtools_version} \
-&& mv htslib-${htslib_version} htslib \
-&& cd htslib \
-&& autoreconf -i \
-&& ./configure \
-&& make \
-&& make install \
-&& cd .. \
-&& make \
-&& mv bin/* /usr/local/bin \
-&& chmod +x /usr/local/bin/fqtools \
-&& cd .. \
-&& rm -r fqtools-${fqtools_version}
-
-RUN curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v${bedtools_version}/bedtools-${bedtools_version}.tar.gz | tar -xz \
-&& make -C bedtools2 \
-&& mv bedtools2/bin/* /usr/local/bin \
-&& rm -r bedtools2
-
-RUN curl -fsSL https://sourceforge.net/projects/bowtie-bio/files/bowtie2/${bowtie2_version}/bowtie2-${bowtie2_version}-source.zip -o bowtie2-${bowtie2_version}-source.zip \
-&& unzip bowtie2-${bowtie2_version}-source.zip \
-&& make -C bowtie2-${bowtie2_version} prefix=/usr/local install \
-&& rm -r bowtie2-${bowtie2_version} \
-&& rm bowtie2-${bowtie2_version}-source.zip
-
-RUN curl -fsSL https://github.com/OpenGene/fastp/archive/v${fastp_version}.tar.gz | tar -xz \
-&& cd fastp-${fastp_version} \
-&& make \
-&& make install \
-&& cd .. \
-&& rm -r fastp-${fastp_version}
-
-RUN wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${fastqc_version}.zip \
-&& unzip fastqc_v${fastqc_version}.zip \
-&& chmod +x FastQC/fastqc \
-&& mv FastQC/* /usr/local/bin \
-&& rm fastqc_v${fastqc_version}.zip \
-&& rm -r FastQC
-
-RUN curl -fsSL https://github.com/DerrickWood/kraken2/archive/v${kraken2_version}.tar.gz | tar -xz \
-&& cd kraken2-${kraken2_version} \
-&& ./install_kraken2.sh /usr/local/bin \
-&& cd ..
-
-RUN curl -fsSL https://github.com/ArthurVM/Afanc/archive/refs/tags/v${afanc_version}-alpha.tar.gz | tar -xz \
-&& cd Afanc-${afanc_version}-alpha \
-&& pip3 install ./ \
-&& cd .. \
-&& curl -fsSL "https://github.com/marbl/Mash/releases/download/v${mash_version}/mash-Linux64-v${mash_version}.tar" | tar -x \
-&& mv mash-Linux64-v${mash_version}/mash /usr/local/bin \
-&& rm -r mash-Linux* \
-&& wget https://github.com/ParBLiSS/FastANI/releases/download/v${fastani_version}/fastANI-Linux64-v${fastani_version}.zip \
-&& unzip fastANI-Linux64-v${fastani_version}.zip \
-&& mv fastANI /usr/local/bin
-
-RUN sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \
-&& mkdir -p /opt/edirect \
-&& mv /root/edirect/* /opt/edirect
-
-RUN git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex \
-&& make -C mccortex \
-&& mv mccortex /usr/local/bin \
-&& curl -fsSL mykrobe-${mykrobe_version}.tar.gz https://github.com/Mykrobe-tools/mykrobe/archive/v${mykrobe_version}.tar.gz | tar -xz \
-&& cd mykrobe-${mykrobe_version} \
-&& pip3 install requests \
-&& pip3 install . \
-&& ln -s /usr/local/bin/mccortex/bin/mccortex31 /usr/local/lib/python3.8/dist-packages/mykrobe/cortex/mccortex31 \
-&& mykrobe panels update_metadata \
-&& mykrobe panels update_species all \
-&& cd ..
-
-RUN curl -fsSL https://github.com/lh3/bwa/archive/v${bwa_version}.tar.gz | tar -C /usr/local/bin -xz \
-&& make -C /usr/local/bin/bwa-${bwa_version} \
-&& chmod +x /usr/local/bin/bwa-${bwa_version}/bwa
-
-RUN unset DEBIAN_FRONTEND
-
-ENV LC_ALL en_US.UTF-8 \
-LANG en_US.UTF-8 \
-LANGUAGE en_US.UTF-8
-
diff --git a/docker/Dockerfile.tbprofiler-0.9.8.1 b/docker/Dockerfile.tbprofiler-0.9.8.1
deleted file mode 100644
index b1a8853..0000000
--- a/docker/Dockerfile.tbprofiler-0.9.8.1
+++ /dev/null
@@ -1,62 +0,0 @@
-FROM ubuntu:focal
-
-#copy the reference genome to pre-compute our index
-COPY resources/tuberculosis.fasta /data/tuberculosis.fasta
-
-ENV tbdb_version=a5e1d48 \
-    tbprofiler_version=6.2.1 \
-    TMPDIR="."
-
-#USER root
-WORKDIR /
-ENV TMPDIR="/data"
-ARG TBPROFILER_VER="6.2.1"
-
-# this version is the shortened commit hash on the `master` branch here https://github.com/jodyphelan/tbdb/
-# commits are found on https://github.com/jodyphelan/tbdb/commits/master
-# this was the latest commit as of 2024-05-21
-ARG TBDB_VER="a5e1d48"
-
-# LABEL instructions tag the image with metadata that might be important to the user
-LABEL base.image="ubuntu:focal"
-LABEL dockerfile.version="0.9.8.1"
-LABEL software="tbprofiler"
-LABEL software.version="${TBPROFILER_VER}"
-LABEL description="The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using bcftools. These variants are then compared to a drug-resistance database."
-LABEL maintainer3="Tom Whalley"
-LABEL maintainer3.email="twhalley93@gmail.com"
-
-#set env for root prefix
-ENV MAMBA_ROOT_PREFIX="/opt/conda"
-
-RUN apt-get update && apt-get install -y apt-utils wget bzip2 curl
-RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest| tar -xvj bin/micromamba \
-    && touch /root/.bashrc \
-    && ./bin/micromamba shell init -s bash -p /opt/conda  \
-    && grep -v '[ -z "\$PS1" ] && return' /root/.bashrc  > /opt/conda/bashrc   # this line has been modified \
-    && apt-get clean autoremove --yes \
-    && rm -rf /var/lib/{apt,dpkg,cache,log}
-
-
-# install tb-profiler via bioconda; install into 'base' conda env
-RUN micromamba install --yes --name base --channel conda-forge --channel bioconda  \
-    tb-profiler=${TBPROFILER_VER}
-
-RUN micromamba install --yes --name base --channel conda-forge --channel bioconda gatk4 
-RUN micromamba install --yes --name base --channel conda-forge --channel bioconda samtools 
-RUN micromamba install --yes --name base --channel conda-forge jq
-RUN micromamba clean --all --yes
-
-# hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time
-ENV PATH="/opt/conda/bin:${PATH}"
-
-
-# Version of database can be confirmed at /opt/conda/share/tbprofiler/tbdb.version.json
-# can also run 'tb-profiler list_db' to find the same version info
-# In 5.0.1 updating_tbdb does not work with tb-profiler update_tbdb --commit ${TBDB_VER}
-
-WORKDIR /data
-
-#wants full path to reference
-RUN tb-profiler update_tbdb --match_ref /data/tuberculosis.fasta --commit ${TBDB_VER}
-
diff --git a/docker/Dockerfile.vcfpredict-0.9.8 b/docker/Dockerfile.vcfpredict-0.9.8
deleted file mode 100644
index 9de1bb7..0000000
--- a/docker/Dockerfile.vcfpredict-0.9.8
+++ /dev/null
@@ -1,27 +0,0 @@
-FROM ubuntu:20.04
-
-LABEL maintainer="pricea35@cardiff.ac.uk" \
-about.summary="container for the vcf predict workflow"
-
-#add run-vcf to container
-COPY bin/ /opt/bin/
-ENV PATH=/opt/bin:$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/JeremyWesthead/VCFMIX.git \
-&& cd VCFMIX \
-&& git checkout ${vcfmix_version} \
-&& pip3 install recursive_diff \
-&& pip3 install awscli \
-&& pip3 install . \
-&& cp -r data /usr/local/lib/python3.8/dist-packages \
-&& cd ..
diff --git a/singularity/Singularity.clockwork-0.9.8 b/singularity/Singularity.clockwork-0.9.8
deleted file mode 100644
index 0e13714..0000000
--- a/singularity/Singularity.clockwork-0.9.8
+++ /dev/null
@@ -1,154 +0,0 @@
-Bootstrap: docker
-From: debian:buster
-Stage: spython-base
-
-%files
-bin/ /opt/bin/
-%labels
-maintainer="pricea35@cardiff.ac.uk" 
-about.summary="container for the clockwork workflow"
-%post
-
-
-samtools_version=1.12
-htslib_version=1.12
-bcftools_version=1.12
-minimap2_version=2.17
-picard_version=2.18.16
-gramtools_version=8af53f6c8c0d72ef95223e89ab82119b717044f2
-vt_version=2187ff6347086e38f71bd9f8ca622cd7dcfbb40c
-minos_version=0.11.0
-cortex_version=3a235272e4e0121be64527f01e73f9e066d378d3
-vcftools_version=0.1.15
-mccortex_version=97aba198d632ee98ac1aa496db33d1a7a8cb7e51
-stampy_version=1.0.32r3761
-python_version=3.6.5
-clockwork_version=2364dec4cbf25c844575e19e8fe0a319d10721b5
-
-PACKAGES="procps curl git build-essential wget zlib1g-dev pkg-config jq r-base-core rsync autoconf libncurses-dev libbz2-dev liblzma-dev libcurl4-openssl-dev cmake tabix libvcflib-tools libssl-dev software-properties-common perl locales locales-all"
-PYTHON="python2.7 python-dev"
-
-PATH=/opt/bin:$PATH
-
-
-apt-get update \
-&& 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 \
-&& wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add - \
-&& add-apt-repository --yes https://adoptopenjdk.jfrog.io/adoptopenjdk/deb/ \
-&& apt-get update && apt-get install -y adoptopenjdk-8-hotspot
-
-
-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}
-
-
-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
-
-
-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}
-
-
-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 ${clockwork_version} \
-&& cd python \
-&& pip3 install . \
-&& chmod +x scripts/clockwork
-
-CLOCKWORK_CORTEX_DIR=/cortex
-PATH=${PATH}:/clockwork/python/scripts
-PICARD_JAR=/usr/local/bin/picard.jar
-
-LC_ALL=en_US.UTF-8
-LANG=en_US.UTF-8
-LANGUAGE=en_US.UTF-8
-
-%environment
-export samtools_version=1.12
-export htslib_version=1.12
-export bcftools_version=1.12
-export minimap2_version=2.17
-export picard_version=2.18.16
-export gramtools_version=8af53f6c8c0d72ef95223e89ab82119b717044f2
-export vt_version=2187ff6347086e38f71bd9f8ca622cd7dcfbb40c
-export minos_version=0.11.0
-export cortex_version=3a235272e4e0121be64527f01e73f9e066d378d3
-export vcftools_version=0.1.15
-export mccortex_version=97aba198d632ee98ac1aa496db33d1a7a8cb7e51
-export stampy_version=1.0.32r3761
-export python_version=3.6.5
-export clockwork_version=2364dec4cbf25c844575e19e8fe0a319d10721b5
-export 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"
-export PYTHON="python2.7 python-dev"
-export PATH=/opt/bin:$PATH
-export CLOCKWORK_CORTEX_DIR=/cortex
-export PATH=${PATH}:/clockwork/python/scripts
-export PICARD_JAR=/usr/local/bin/picard.jar
-export LC_ALL=en_US.UTF-8
-export LANG=en_US.UTF-8
-export LANGUAGE=en_US.UTF-8
-%runscript
-exec /bin/bash "$@"
-%startscript
-exec /bin/bash "$@"
diff --git a/singularity/Singularity.preprocessing-0.9.8 b/singularity/Singularity.preprocessing-0.9.8
deleted file mode 100644
index 6ec7c12..0000000
--- a/singularity/Singularity.preprocessing-0.9.8
+++ /dev/null
@@ -1,165 +0,0 @@
-Bootstrap: docker
-From: ubuntu:focal
-Stage: spython-base
-
-%files
-bin/ /opt/bin/
-%labels
-maintainer="pricea35@cardiff.ac.uk" 
-about.summary="container for the preprocessing workflow"
-%post
-
-
-samtools_version=1.12
-bcftools_version=1.12
-htslib_version=1.12
-bedtools_version=2.29.2
-bowtie2_version=2.4.2
-fastp_version=0.20.1
-fastqc_version=0.11.9
-fqtools_version=2.3
-kraken2_version=2.1.1
-afanc_version=0.10.2
-mykrobe_version=0.12.1
-bwa_version=0.7.17
-mash_version=2.3
-fastani_version=1.33
-
-PACKAGES="procps curl git wget build-essential zlib1g-dev libncurses-dev libz-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libgsl-dev rsync unzip ncbi-blast+ pigz jq libtbb-dev openjdk-11-jre-headless autoconf r-base-core locales locales-all"
-PYTHON="python3 python3-pip python3-dev"
-PYTHON_PACKAGES="biopython awscli boto3"
-
-PATH=${PATH}:/usr/local/bin/mccortex/bin:/usr/local/bin/bwa-${bwa_version}:/opt/edirect
-LD_LIBRARY_PATH=/usr/local/lib
-
-export DEBIAN_FRONTEND="noninteractive"
-
-PATH=/opt/bin:$PATH
-
-apt-get update \
-&& DEBIAN_FRONTEND="noninteractive" apt-get install -y $PACKAGES $PYTHON \
-&& pip3 install --upgrade pip \
-&& pip3 install $PYTHON_PACKAGES \
-&& ln -s /usr/bin/python3 /usr/bin/python
-
-curl -fsSL https://github.com/samtools/samtools/archive/${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-${bcftools_version}
-
-curl -fsSL https://github.com/alastair-droop/fqtools/archive/v${fqtools_version}.tar.gz | tar -xz \
-&& mv htslib-${htslib_version} fqtools-${fqtools_version} \
-&& cd fqtools-${fqtools_version} \
-&& mv htslib-${htslib_version} htslib \
-&& cd htslib \
-&& autoreconf -i \
-&& ./configure \
-&& make \
-&& make install \
-&& cd .. \
-&& make \
-&& mv bin/* /usr/local/bin \
-&& chmod +x /usr/local/bin/fqtools \
-&& cd .. \
-&& rm -r fqtools-${fqtools_version}
-
-curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v${bedtools_version}/bedtools-${bedtools_version}.tar.gz | tar -xz \
-&& make -C bedtools2 \
-&& mv bedtools2/bin/* /usr/local/bin \
-&& rm -r bedtools2
-
-curl -fsSL https://sourceforge.net/projects/bowtie-bio/files/bowtie2/${bowtie2_version}/bowtie2-${bowtie2_version}-source.zip -o bowtie2-${bowtie2_version}-source.zip \
-&& unzip bowtie2-${bowtie2_version}-source.zip \
-&& make -C bowtie2-${bowtie2_version} prefix=/usr/local install \
-&& rm -r bowtie2-${bowtie2_version} \
-&& rm bowtie2-${bowtie2_version}-source.zip
-
-curl -fsSL https://github.com/OpenGene/fastp/archive/v${fastp_version}.tar.gz | tar -xz \
-&& cd fastp-${fastp_version} \
-&& make \
-&& make install \
-&& cd .. \
-&& rm -r fastp-${fastp_version}
-
-wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${fastqc_version}.zip \
-&& unzip fastqc_v${fastqc_version}.zip \
-&& chmod +x FastQC/fastqc \
-&& mv FastQC/* /usr/local/bin \
-&& rm fastqc_v${fastqc_version}.zip \
-&& rm -r FastQC
-
-curl -fsSL https://github.com/DerrickWood/kraken2/archive/v${kraken2_version}.tar.gz | tar -xz \
-&& cd kraken2-${kraken2_version} \
-&& ./install_kraken2.sh /usr/local/bin \
-&& cd ..
-
-curl -fsSL https://github.com/ArthurVM/Afanc/archive/refs/tags/v${afanc_version}-alpha.tar.gz | tar -xz \
-&& cd Afanc-${afanc_version}-alpha \
-&& pip3 install ./ \
-&& cd .. \
-&& curl -fsSL "https://github.com/marbl/Mash/releases/download/v${mash_version}/mash-Linux64-v${mash_version}.tar" | tar -x \
-&& mv mash-Linux64-v${mash_version}/mash /usr/local/bin \
-&& rm -r mash-Linux* \
-&& wget https://github.com/ParBLiSS/FastANI/releases/download/v${fastani_version}/fastANI-Linux64-v${fastani_version}.zip \
-&& unzip fastANI-Linux64-v${fastani_version}.zip \
-&& mv fastANI /usr/local/bin
-
-sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \
-&& mkdir -p /opt/edirect \
-&& mv /root/edirect/* /opt/edirect
-
-git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex \
-&& make -C mccortex \
-&& mv mccortex /usr/local/bin \
-&& curl -fsSL mykrobe-${mykrobe_version}.tar.gz https://github.com/Mykrobe-tools/mykrobe/archive/v${mykrobe_version}.tar.gz | tar -xz \
-&& cd mykrobe-${mykrobe_version} \
-&& pip3 install requests \
-&& pip3 install . \
-&& ln -s /usr/local/bin/mccortex/bin/mccortex31 /usr/local/lib/python3.8/dist-packages/mykrobe/cortex/mccortex31 \
-&& mykrobe panels update_metadata \
-&& mykrobe panels update_species all \
-&& cd ..
-
-curl -fsSL https://github.com/lh3/bwa/archive/v${bwa_version}.tar.gz | tar -C /usr/local/bin -xz \
-&& make -C /usr/local/bin/bwa-${bwa_version} \
-&& chmod +x /usr/local/bin/bwa-${bwa_version}/bwa
-
-unset DEBIAN_FRONTEND
-
-LC_ALL=en_US.UTF-8
-LANG=en_US.UTF-8
-LANGUAGE=en_US.UTF-8
-
-%environment
-export samtools_version=1.12
-export bcftools_version=1.12
-export htslib_version=1.12
-export bedtools_version=2.29.2
-export bowtie2_version=2.4.2
-export fastp_version=0.20.1
-export fastqc_version=0.11.9
-export fqtools_version=2.3
-export kraken2_version=2.1.1
-export afanc_version=0.10.2
-export mykrobe_version=0.12.1
-export bwa_version=0.7.17
-export mash_version=2.3
-export fastani_version=1.33
-export PACKAGES="procps curl git wget build-essential zlib1g-dev libncurses-dev libz-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libgsl-dev rsync unzip ncbi-blast+ pigz jq libtbb-dev openjdk-11-jre-headless autoconf r-base-core locales locales-all"
-export PYTHON="python3 python3-pip python3-dev"
-export PYTHON_PACKAGES="biopython awscli boto3"
-export PATH=${PATH}:/usr/local/bin/mccortex/bin:/usr/local/bin/bwa-${bwa_version}:/opt/edirect
-export LD_LIBRARY_PATH=/usr/local/lib
-export PATH=/opt/bin:$PATH
-export LC_ALL=en_US.UTF-8
-export LANG=en_US.UTF-8
-export LANGUAGE=en_US.UTF-8
-%runscript
-exec /bin/bash "$@"
-%startscript
-exec /bin/bash "$@"
diff --git a/singularity/Singularity.tbprofiler-0.9.8.1 b/singularity/Singularity.tbprofiler-0.9.8.1
deleted file mode 100644
index de733db..0000000
--- a/singularity/Singularity.tbprofiler-0.9.8.1
+++ /dev/null
@@ -1,83 +0,0 @@
-Bootstrap: docker
-From: ubuntu:focal
-Stage: spython-base
-
-%files
-resources/tuberculosis.fasta /data/tuberculosis.fasta
-%labels
-base.image="ubuntu:focal"
-dockerfile.version="0.9.8.1"
-software="tbprofiler"
-software.version="${TBPROFILER_VER}"
-description="The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using bcftools. These variants are then compared to a drug-resistance database."
-maintainer3="Tom Whalley"
-maintainer3.email="twhalley93@gmail.com"
-%post
-
-#copy the reference genome to pre-compute our index
-
-tbdb_version=a5e1d48
-tbprofiler_version=6.2.1
-TMPDIR="."
-
-#USER root
-mkdir -p /
-cd /
-TMPDIR="/data"
-TBPROFILER_VER="6.2.1"
-
-# this version is the shortened commit hash on the `master` branch here https://github.com/jodyphelan/tbdb/
-# commits are found on https://github.com/jodyphelan/tbdb/commits/master
-# this was the latest commit as of 2024-05-21
-TBDB_VER="a5e1d48"
-
-# LABEL instructions tag the image with metadata that might be important to the user
-
-#set env for root prefix
-MAMBA_ROOT_PREFIX="/opt/conda"
-
-apt-get update && apt-get install -y apt-utils wget bzip2 curl
-curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest| tar -xvj bin/micromamba \
-&& touch /root/.bashrc \
-&& ./bin/micromamba shell init -s bash -p /opt/conda  \
-&& grep -v '[ -z "\$PS1" ] && return' /root/.bashrc  > /opt/conda/bashrc   # this line has been modified \
-&& apt-get clean autoremove --yes \
-&& rm -rf /var/lib/{apt,dpkg,cache,log}
-
-
-# install tb-profiler via bioconda; install into 'base' conda env
-micromamba install --yes --name base --channel conda-forge --channel bioconda  \
-tb-profiler=${TBPROFILER_VER}
-
-micromamba install --yes --name base --channel conda-forge --channel bioconda gatk4
-micromamba install --yes --name base --channel conda-forge --channel bioconda samtools
-micromamba install --yes --name base --channel conda-forge jq
-micromamba clean --all --yes
-
-# hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time
-PATH="/opt/conda/bin:${PATH}"
-
-
-# Version of database can be confirmed at /opt/conda/share/tbprofiler/tbdb.version.json
-# can also run 'tb-profiler list_db' to find the same version info
-# In 5.0.1 updating_tbdb does not work with tb-profiler update_tbdb --commit ${TBDB_VER}
-
-mkdir -p /data
-cd /data
-
-#wants full path to reference
-tb-profiler update_tbdb --match_ref /data/tuberculosis.fasta --commit ${TBDB_VER}
-
-%environment
-export tbdb_version=a5e1d48
-export tbprofiler_version=6.2.1
-export TMPDIR="."
-export TMPDIR="/data"
-export MAMBA_ROOT_PREFIX="/opt/conda"
-export PATH="/opt/conda/bin:${PATH}"
-%runscript
-cd /data
-exec /bin/bash "$@"
-%startscript
-cd /data
-exec /bin/bash "$@"
diff --git a/singularity/Singularity.vcfpredict-0.9.8 b/singularity/Singularity.vcfpredict-0.9.8
deleted file mode 100644
index 0146e7d..0000000
--- a/singularity/Singularity.vcfpredict-0.9.8
+++ /dev/null
@@ -1,41 +0,0 @@
-Bootstrap: docker
-From: ubuntu:20.04
-Stage: spython-base
-
-%files
-bin/ /opt/bin/
-%labels
-maintainer="pricea35@cardiff.ac.uk" 
-about.summary="container for the vcf predict workflow"
-%post
-
-
-#add run-vcf to container
-PATH=/opt/bin:$PATH
-
-PACKAGES="procps curl wget git build-essential libhdf5-dev libffi-dev r-base-core jq"
-PYTHON="python3 python3-pip python3-dev"
-
-vcfmix_version=d4693344bf612780723e39ce27c8ae3868f95417
-#apt updates
-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/JeremyWesthead/VCFMIX.git \
-&& cd VCFMIX \
-&& git checkout ${vcfmix_version} \
-&& pip3 install recursive_diff \
-&& pip3 install awscli \
-&& pip3 install . \
-&& cp -r data /usr/local/lib/python3.8/dist-packages \
-&& cd ..
-%environment
-export PATH=/opt/bin:$PATH
-export PACKAGES="procps curl wget git build-essential libhdf5-dev libffi-dev r-base-core jq"
-export PYTHON="python3 python3-pip python3-dev"
-export vcfmix_version=d4693344bf612780723e39ce27c8ae3868f95417
-%runscript
-exec /bin/bash "$@"
-%startscript
-exec /bin/bash "$@"