Auto-Save Index Files Alongside BAMs

.dockstore.yml

@@ -108,3 +108,91 @@ workflows:
   subclass: wdl
   primaryDescriptorPath: /wdl/PBMASIsoSeqDemultiplex.wdl
   testParameterFiles:
+- name: SRBamToFq
+  subclass: wdl
+  primaryDescriptorPath: /wdl/SRBamToFq.wdl
+  testParameterFiles:
+- name: SRIndexBam
+  subclass: wdl
+  primaryDescriptorPath: /wdl/SRIndexBam.wdl
+  testParameterFiles:
+- name: SRWholeGenome
+  subclass: wdl
+  primaryDescriptorPath: /wdl/SRWholeGenome.wdl
+  testParameterFiles:
+- name: SRFlowcell
+  subclass: wdl
+  primaryDescriptorPath: /wdl/SRFlowcell.wdl
+  testParameterFiles:
+- name: SRJointCallGVCFsWithGenomicsDB
+  subclass: wdl
+  primaryDescriptorPath: /wdl/SRJointCallGVCFsWithGenomicsDB.wdl
+  testParameterFiles:
+- name: LRJointCallGVCFsWithGenomicsDB
+  subclass: wdl
+  primaryDescriptorPath: /wdl/LRJointCallGVCFsWithGenomicsDB.wdl
+  testParameterFiles:
+- name: LRJointCallGVCFs
+  subclass: wdl
+  primaryDescriptorPath: /wdl/LRJointCallGVCFs.wdl
+  testParameterFiles:
+- name: ConvertToHailMT
+  subclass: wdl
+  primaryDescriptorPath: /wdl/ConvertToHailMT.wdl
+  testParameterFiles:
+- name: ConvertToZarrStore
+  subclass: wdl
+  primaryDescriptorPath: /wdl/ConvertToZarrStore.wdl
+  testParameterFiles:
+- name: LRConvertBCF
+  subclass: wdl
+  primaryDescriptorPath: /wdl/LRConvertBCF.wdl
+  testParameterFiles:
+- name: BenchmarkVCFs
+  subclass: wdl
+  primaryDescriptorPath: /wdl/BenchmarkVCFs.wdl
+  testParameterFiles:
+- name: CompareVcfBenchmarks
+  subclass: wdl
+  primaryDescriptorPath: /wdl/CompareVcfBenchmarks.wdl
+  testParameterFiles:
+- name: PanelProcessMalariaBarcodesForRh
+  subclass: wdl
+  primaryDescriptorPath: /wdl/PanelProcessMalariaBarcodesForRh.wdl
+  testParameterFiles:
+- name: ProcessMalariaBarcodesDemo
+  subclass: wdl
+  primaryDescriptorPath: /wdl/ProcessMalariaBarcodesDemo.wdl
+  testParameterFiles:
+- name: ExtractRegionsFromBam
+  subclass: wdl
+  primaryDescriptorPath: /wdl/ExtractRegionsFromBam.wdl
+  testParameterFiles:
+- name: PfalciparumDrugResistanceSummary
+  subclass: wdl
+  primaryDescriptorPath: /wdl/PfalciparumDrugResistanceSummary.wdl
+  testParameterFiles:
+- name: SRWholeGenome_Pf_Niare_VQSR
+  subclass: wdl
+  primaryDescriptorPath: /wdl/SRWholeGenome_Pf_Niare_VQSR.wdl
+  testParameterFiles:
+- name: SRWholeGenome_Pf_Niare_VETS
+  subclass: wdl
+  primaryDescriptorPath: /wdl/SRWholeGenome_Pf_Niare_VETS.wdl
+  testParameterFiles:
+- name: SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VQSR
+  subclass: wdl
+  primaryDescriptorPath: /wdl/SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VQSR.wdl
+  testParameterFiles:
+- name: SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VETS
+  subclass: wdl
+  primaryDescriptorPath: /wdl/SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VETS.wdl
+  testParameterFiles:
+- name: ExpandedDrugResistanceMarkerExtraction
+  subclass: wdl
+  primaryDescriptorPath: /wdl/ExpandedDrugResistanceMarkerExtraction.wdl
+  testParameterFiles:
+- name: ExpandedDrugResistanceMarkerAggregation
+  subclass: wdl
+  primaryDescriptorPath: /wdl/ExpandedDrugResistanceMarkerAggregation.wdl
+  testParameterFiles:

BRANCH_IS_DEPRECATED.txt

@@ -0,0 +1,7 @@
+THIS BRANCH IS DEPRECATED.
+
+AS OF 2024 Jan 09, ALL CODE IN THIS BRANCH HAS BEEN MERGED TO MAIN.
+
+THIS BRANCH SHALL CONTINUE TO EXIST AS A REFERENCE UNTIL
+JONN IS BACK FROM PATERNITY LEAVE.
+

README.md

@@ -1,4 +1,4 @@
-[![Generic badge](https://img.shields.io/badge/version-3.0.57-blue.svg)](https://shields.io/)
+[![Generic badge](https://img.shields.io/badge/version-3.0.59-blue.svg)](https://shields.io/)
 ![CI/CD](https://github.com/broadinstitute/long-read-pipelines/workflows/CI/CD/badge.svg)
 ![Nightly](https://github.com/broadinstitute/long-read-pipelines/workflows/Nightly/badge.svg)
 

VERSION

@@ -1,2 +1,2 @@
 
-version=3.0.57
+version=3.0.59

docker/lr-functional-annotation/Dockerfile

@@ -0,0 +1,70 @@
+# Start with a good base python3 image:
+FROM ubuntu:20.04
+MAINTAINER Jonn Smith <[email protected]>
+
+# Make sure we don't need to interact with any package installations:
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Set the working directory to /
+WORKDIR /
+
+################################################################################
+# Install system packages:
+
+# Make sure we can actually talk to package repos:
+RUN apt-get update 
+RUN apt-get install -y apt-utils
+RUN apt-get -y upgrade
+
+RUN apt-get update && apt-get -y upgrade
+
+# Development / prereqs for building software:
+# Utilities / tools:
+# Get libcurses:
+# install gsutil requirements:
+RUN apt-get -y install make gcc g++ autoconf sudo && \
+    apt-get -y install git bash vim time bc sed perl wget curl bzip2 man unzip && \
+    apt-get -y install liblzma-dev libbz2-dev libncurses5-dev libncursesw5-dev && \
+    apt-get --allow-releaseinfo-change update && \
+    apt install -y curl git-lfs time datamash
+
+# Install python:
+RUN apt-get install -y python python3 python3-pip
+
+# Setup crcmodc for gsutil:
+RUN apt-get install -y gcc python3-dev python3-setuptools && \
+			pip3 uninstall -y crcmod && \
+			pip3 install --no-cache-dir -U crcmod
+
+# install gsutil:
+RUN curl https://sdk.cloud.google.com | bash
+
+# Get Java:
+# Install OpenJDK-8
+RUN apt-get update && \
+    apt-get install -y openjdk-11-jdk && \
+    apt-get install -y ant && \
+    apt-get clean
+
+# Fix certificate issues
+RUN apt-get update && \
+    apt-get install ca-certificates-java && \
+    apt-get clean && \
+    update-ca-certificates -f
+
+# Setup JAVA_HOME -- useful for docker commandline
+ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
+RUN export JAVA_HOME
+
+# Get snPEff
+RUN wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip && \
+	unzip snpEff_latest_core.zip
+
+# Get tabix (for bgzip):
+RUN apt-get install -y tabix
+
+################################################################################
+# Final runtime configuration:
+# Let's start at the root:
+WORKDIR /
+

docker/lr-functional-annotation/Makefile

@@ -0,0 +1,17 @@
+IMAGE_NAME = lr-functional-annotation
+VERSION = 0.0.1
+
+TAG1 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):$(VERSION)
+TAG2 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):latest
+
+all: | build push
+
+build:
+	docker build -t $(TAG1) -t $(TAG2) .
+
+build_no_cache:
+	docker build --no-cache -t $(TAG1) -t $(TAG2) .
+
+push:
+	docker push $(TAG1)
+	docker push $(TAG2)

docker/lr-malaria/Dockerfile

@@ -0,0 +1,27 @@
+FROM continuumio/miniconda3:22.11.1
+
+MAINTAINER Jonn Smith
+
+# copy other resources
+COPY ./environment.yml /
+
+# install conda packages
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH=/root/google-cloud-sdk/bin/:${PATH}
+
+# install gsutil
+RUN apt-get --allow-releaseinfo-change update
+RUN apt install -y curl git-lfs time datamash
+RUN curl https://sdk.cloud.google.com | bash
+
+# Setup crcmodc for gsutil:
+RUN apt-get install -y gcc python3-dev python3-setuptools && \
+			pip3 uninstall -y crcmod && \
+			pip3 install --no-cache-dir -U crcmod
+
+# copy python scripts
+COPY python/* /python_scripts/
+RUN chmod +x /python_scripts/*
+
+# activate conda environment
+RUN echo "source activate lr-malaria" > ~/.bashrc

docker/lr-malaria/Makefile

@@ -0,0 +1,17 @@
+IMAGE_NAME = lr-malaria
+VERSION = 0.0.1
+
+TAG1 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):$(VERSION)
+TAG2 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):latest
+
+all: | build push
+
+build:
+	docker build -t $(TAG1) -t $(TAG2) .
+
+build_no_cache:
+	docker build --no-cache -t $(TAG1) -t $(TAG2) .
+
+push:
+	docker push $(TAG1)
+	docker push $(TAG2)

docker/lr-malaria/environment.yml

@@ -0,0 +1,22 @@
+name: lr-malaria
+channels:
+  - default
+  - bioconda
+  - anaconda
+dependencies:
+  - python=3.6
+  - cython
+  - pip
+  - pip:
+    - numpy
+    - scipy
+    - pandas
+    - seaborn
+    - statsmodels
+    - networkx
+    - matplotlib
+    - patsy
+    - openpyxl
+    - scikit-learn
+    - numpyencoder
+    - tqdm