Hangsu phasing

.dockstore.yml

@@ -96,3 +96,15 @@ workflows:
 - name: CleanupIntermediate
   subclass: wdl
   primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/CleanupIntermediate.wdl
+- name: StatisticalPhasing
+  subclass: wdl
+  primaryDescriptorPath: /wdl/pipelines/PacBio/Assembly
+- name: BandagePlotGraph
+  subclass: wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/BandagePlotGraph.wdl
+- name: ConvertToHailMTT2T
+  subclass: wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/ConvertToHailMTT2T.wdl
+- name: MergePhasedVCF
+  subclass: wdl
+  primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/MergePhasedVCF.wdl

docker/lr-bandage/Dockerfile

@@ -0,0 +1,31 @@
+FROM flowcraft/bandage:0.8.1
+
+# ARG SAMTOOLS_VERSION=1.15.1
+# ARG BCFTOOLS_VERSION=1.15.1
+
+# ARG DEBIAN_FRONTEND=noninteractive
+# RUN apt-get -qqy update --fix-missing && \
+#     apt-get -qqy dist-upgrade && \
+#     apt-get -qqy install --no-install-recommends \
+#                  ca-certificates \
+#                  libbz2-dev \
+#                  libcurl4-openssl-dev \
+#                  liblzma-dev \
+#                  libncurses5-dev \
+#                  autoconf \
+#                  automake \
+#                  bzip2 \
+#                  gcc \
+#                  g++ \
+#                  make \
+#                  wget \
+#                  zlib1g-dev && \
+
+#     wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
+#     tar xjf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
+#     cd samtools-${SAMTOOLS_VERSION} && ./configure --without-curses --enable-libcurl && make -s all all-htslib && make install install-htslib && cd - && \
+#     rm -rf samtools-${SAMTOOLS_VERSION}* && \
+#     wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
+#     tar xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
+#     cd bcftools-${BCFTOOLS_VERSION} && ./configure --without-curses && make -s && make install && cd - && \
+#     rm -rf bcftools-${BCFTOOLS_VERSION}*