🦄 adding minimap2 and nanocount for ONT wf (#238)

* adding minimap2 and nanocount for ONT wf

* update docker table (#239)

Co-authored-by: wongjessica93 <[email protected]>

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: wongjessica93 <[email protected]>

README.md

@@ -101,7 +101,9 @@ lumpy-sv|0.3.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/lumpy-sv:0.3.0
 manta|1.4|docker pull pgc-images.sbgenomics.com/d3b-bixu/manta:1.4
 manta|1.6.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/manta:1.6.0
 mend_qc|latest|docker pull pgc-images.sbgenomics.com/d3b-bixu/mend_qc:latest
+minimap2|v2.28|docker pull pgc-images.sbgenomics.com/d3b-bixu/minimap2:v2.28
 msisensor|1.1.a|docker pull pgc-images.sbgenomics.com/d3b-bixu/msisensor:1.1.a
+nanocount|v1.1.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/nanocount:v1.1.0
 ngscheckmate|1.3|docker pull pgc-images.sbgenomics.com/d3b-bixu/ngscheckmate:1.3
 octopus|0.6.3-beta|docker pull pgc-images.sbgenomics.com/d3b-bixu/octopus:0.6.3-beta
 pbta-splicing|0.1|docker pull pgc-images.sbgenomics.com/d3b-bixu/pbta-splicing:0.1

minimap2/v2.28/Dockerfile

@@ -0,0 +1,20 @@
+FROM --platform=linux/amd64 ubuntu:22.04
+
+LABEL maintainer="Jessica Wong <[email protected]>"
+LABEL description="minimap2"
+
+RUN apt update && apt install -y \
+    wget \
+    build-essential \
+    samtools
+
+ENV MINIMAP2_VERSION 2.28
+
+RUN wget https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2 \
+    && tar -jxvf minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2
+
+WORKDIR /minimap2-${MINIMAP2_VERSION}_x64-linux
+
+RUN cp minimap2 /usr/local/bin/
+
+COPY Dockerfile .

nanocount/v1.1.0/Dockerfile

@@ -0,0 +1,26 @@
+FROM --platform=linux/amd64 ubuntu:22.04
+
+LABEL maintainer="Jessica Wong <[email protected]>"
+LABEL description="nanocount"
+
+RUN apt update && apt install -y \
+    curl \
+    build-essential \
+    zlib1g-dev \
+    liblzma-dev \
+    libbz2-dev \
+    libncurses5-dev \
+    libcurl4-gnutls-dev \
+    libssl-dev \
+    python3 \
+    python3-pip \
+    git
+
+ENV NANOCOUNT_VERSION 1.1.0
+
+RUN curl -sL 'https://github.com/pysam-developers/pysam/archive/refs/tags/v0.22.0.tar.gz' | tar xz && cd pysam-0.22.0 && pip3 install .
+
+RUN pip3 install git+https://github.com/a-slide/NanoCount.git
+
+WORKDIR /
+COPY Dockerfile .