Added Dockstore-related files

.bashrc

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+source /usr/share/modules/init/bash
+module use /modules/gsi/modulator/modulefiles/Ubuntu18.04

Dockerfile

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+FROM modulator:latest
+
+MAINTAINER Fenglin Chen <f73chen@uwaterloo.ca>
+
+# packages should already be set up in modulator:latest
+USER root
+
+# move in the yaml to build modulefiles from
+COPY recipes/sequenza_recipe.yaml /modulator/code/gsi/recipe.yaml
+
+# build the modules and set folder / file permissions
+RUN ./build-local-code /modulator/code/gsi/recipe.yaml --initsh /usr/share/modules/init/sh --output /modules && \
+	find /modules -type d -exec chmod 777 {} \; && \
+	find /modules -type f -exec chmod 777 {} \;
+
+# install required packages
+RUN apt-get -m update && apt-get install -y gzip zip unzip
+
+# add the user
+RUN groupadd -r -g 1000 ubuntu && useradd -r -g ubuntu -u 1000 ubuntu
+USER ubuntu
+
+# copy the setup file to load the modules at startup
+COPY .bashrc /home/ubuntu/.bashrc
+
+# set environment paths for modules
+#ENV BIOCONDUCTOR_ROOT="/modules/gsi/modulator/sw/Ubuntu18.04/bioconductor-3.8-rstats3.6"
+#ENV RSTATS_ROOT="/modules/gsi/modulator/sw/Ubuntu18.04/rstats-3.6"
+#ENV SEQUENZA_ROOT="/modules/gsi/modulator/sw/Ubuntu18.04/sequenza-2.1.2"
+#ENV SEQUENZA_RES_ROOT="/modules/gsi/modulator/sw/Ubuntu18.04/sequenza-res-2.1.2"
+#ENV SEQUENZA_SCRIPTS_ROOT="/modules/gsi/modulator/sw/Ubuntu18.04/sequenza-scripts-2.1.2"
+
+#ENV PATH="/modules/gsi/modulator/sw/Ubuntu18.04/rstats-3.6/bin:/modules/gsi/modulator/sw/Ubuntu18.04/sequenza-scripts-2.1.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
+#ENV MANPATH="/modules/gsi/modulator/sw/Ubuntu18.04/rstats-3.6/share/man"
+#ENV LD_LIBRARY_PATH="/modules/gsi/modulator/sw/Ubuntu18.04/rstats-3.6/lib:/modules/gsi/modulator/sw/Ubuntu18.04/sequenza-2.1.2/lib:/modules/gsi/modulator/sw/Ubuntu18.04/sequenza-scripts-2.1.2/lib:/modules/gsi/modulator/sw/Ubuntu18.04/bioconductor-3.8-rstats3.6/lib"
+#ENV R_LIBS_SITE="/modules/gsi/modulator/sw/Ubuntu18.04/rstats-3.6/lib/R/library:/modules/gsi/modulator/sw/Ubuntu18.04/sequenza-2.1.2/lib/R/library:/modules/gsi/modulator/sw/Ubuntu18.04/sequenza-scripts-2.1.2/lib/R/library:/modules/gsi/modulator/sw/Ubuntu18.04/bioconductor-3.8-rstats3.6/lib/R/library" 
+
+CMD /bin/bash

Dockstore_README.md

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+# dockstore_sequenza
+
+The workflow is made to run in Docker and uploaded to [Dockstore](https://docs.dockstore.org/en/develop/getting-started/getting-started.html).
+You can find OICR's Dockstore page [here](https://dockstore.org/organizations/OICR).
+The Docker container is based on [Modulator](https://gitlab.oicr.on.ca/ResearchIT/modulator), which builds environment modules to set up the docker runtime environment.
+
+### Set Up and Run
+Currently, this WDL must be run with Cromwell. 
+It uses Cromwell configuration files to mount a directory to the docker container.
+The directory contains data modules built with Modulator, which the WDL tasks need to access.
+In addition, you must obtain run files locally and build data modules to a local directory.
+
+#### 1. Build Data Modules
+- Create a local `data_modules/` directory to store the data modules
+    - make sure you have enough disk space
+    - each data module could be 5-30 GB in size
+- In future iterations of the workflow, this process will be simplified
+- Enter the container:
+```
+# Mount this repository as /pipeline/; mount the data module destination directory as /data_modules/
+docker run -it --rm -v [PWD]:/pipeline -v [data_modules]:/data_modules [CONTAINER ID (find in options.json)]
+
+# Copy prerequisite code module YAMLs into the Modulator code directory (code/gsi/)
+cp /pipeline/recipes/sequenza_data_modules_prep.yaml code/gsi/data_modules_recipe_prep.yaml
+
+# Build the prerequisite code modules
+./build-local-code code/gsi/data_modules_recipe_prep.yaml --output /data_modules --initsh /usr/share/modules/init/sh
+
+# Copy data module YAMLs into the Modulator data directory (data/gsi/)
+cp /pipeline/recipes/sequenza_data_modules.yaml data/gsi/data_modules_recipe.yaml
+
+# Build the data modules
+./build-local-data data/gsi/data_modules_recipe.yaml --output /data_modules --initsh /usr/share/modules/init/sh
+
+# Change resulting file permissions
+find /data_modules/ -type d -exec chmod 777 {} \; && \
+find /data_modules/ -type f -exec chmod 777 {} \;
+
+# /data_modules/ should now contain gsi/modulator/modulefiles/Ubuntu18.04/ and gsi/modulator/modulefiles/data/
+```
+For run directories that are not part of modules, copy them from UGE's archive at `/.mounts/labs/gsi/src/`
+
+#### 2. Obtain Files Locally
+In the test json, change file paths like so:
+- File type files should be copied to local
+    - E.g. use scp to copy from UGE
+    - In the json, change the file path from UGE to local path
+- String type files should be copied or moved to the mounted directory, if it's not already part of a module
+    - In the json, change the file path to how the file would be accessed from inside the docker container
+- $MODULE_ROOT paths can stay the same
+```
+# File type files
+# File is copied to local machine
+UGE:       "/.mounts/labs/gsi/testdata/wgsPipeline/input_data/wgsPipeline_test_pcsi/hg19_random.genome.sizes.bed"
+Dockstore: "/home/ubuntu/data/sample_data/callability/hg19_random.genome.sizes.bed"
+
+# String type files
+# /data_modules/ is a directory mounted to the docker container
+UGE:       "/.mounts/labs/gsi/modulator/sw/data/hg19-p13/hg19_random.fa"
+Dockstore: "/data_modules/gsi/modulator/sw/data/hg19-p13/hg19_random.fa"
+
+# Root type paths
+# The value of $MODULE_ROOT changes, but the path stays the same
+UGE:       "$HG19_BWA_INDEX_ROOT/hg19_random.fa"
+Dockstore: "$HG19_BWA_INDEX_ROOT/hg19_random.fa"
+```
+
+#### 3. Run with Cromwell
+Submit the preprocessed subworkflow and modified json to Cromwell, with configs and options attached
+```
+# Validate the wrapper workflow and json
+java -jar $womtool validate [WDL] --inputs [TEST JSON]
+
+# For example:
+java -jar $womtool validate wgsPipeline.wdl --inputs tests/wgsPipeline_test_cre_uge.json
+
+# Submit to Cromwell
+java -Dconfig.file=[CONFIG] -jar $cromwell run [WRAPPER WDL] --inputs [JSON] --options [OPTIONS]
+
+# For example:
+java -Dconfig.file=local.config -jar $cromwell run wgsPipeline.wdl --inputs tests/wgsPipeline_test_cre.json --options options.json
+```

local.config

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+backend {
+  default = "Local"
+  providers {
+    Local {
+      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
+      config {
+        concurrent-job-limit = 10
+        #run-in-background = true
+        runtime-attributes = """
+        String? docker
+        String? docker_volume
+        String? modules
+        """
+        submit = "/usr/bin/env bash ${script}"
+        submit-docker = """
+        docker run \
+        --rm -i \
+        -v ${cwd}:${docker_cwd} \
+        ${"-v " + docker_volume} \
+        ${docker} /bin/bash -c 'source /home/ubuntu/.bashrc; ${"module load " + modules + " || exit 1; "} /bin/bash ${docker_script}'
+        """
+        root = "cromwell-executions"
+        dockerRoot = "/cromwell-executions"
+      }
+    }
+  }
+}
+call-caching {
+  enabled = true
+  invalidate-bad-cache-results = true
+}
+database {
+  profile = "slick.jdbc.HsqldbProfile$"
+  db {
+    driver = "org.hsqldb.jdbcDriver"
+    url = """
+    jdbc:hsqldb:file:/tmp/cromwell-executions/cromwell-db/cromwell-db;
+    shutdown=false;
+    hsqldb.default_table_type=cached;hsqldb.tx=mvcc;
+    hsqldb.result_max_memory_rows=10000;
+    hsqldb.large_data=true;
+    hsqldb.applog=1;
+    hsqldb.lob_compressed=true;
+    hsqldb.script_format=3
+    """
+    connectionTimeout = 120000
+    numThreads = 2
+   }
+}

options.json

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+{
+  "default_runtime_attributes": {
+    "docker": "g3chen/sequenza@sha256:f6ebd82705ecc3bdf5f2fead408333ae60492f36b23259d0730d6c70fc7fbb00",
+    "docker_volume": "/home/ubuntu/Downloads/sample_data:/data"
+  }
+}

recipes/sequenza_data_modules.yaml

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+# sequenza-res/2.1.2
+- name: sequenza-res
+  version: 2.1.2
+  build_type: custom
+  build_args:
+    prereq_type: download
+    prereq_args:
+      sha256: b6604cf111849db6997c4ab0fc618f233fd63fc87a6381491470dfa6b1243bdc
+      url: http://api.gdc.cancer.gov/data/dea893cd-9189-4091-9611-e761a1d31ebe
+    steps:
+      - command: [ "Rscript", "{sequenza-scripts_root}/bin/Generate_plody_priors_table.R", "download" ]
+      - command: [ "cp", "PANCAN_ASCAT_ploidy_prob.Rdata", "{output_dir}/" ]
+  depends:
+    - name: sequenza-scripts
+      version: 2.1.2
+      required_at: build
+    - name: rstats
+      version: 3.6
+      required_at: build

recipes/sequenza_data_modules_prep.yaml

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+# rstats/3.6
+- name: rstats
+  version: 3.6
+  build_type: custom
+  build_args:
+    steps:
+      - build_args:
+          prereq_args:
+            prereq_args:
+              md5: f5003472d58a3d3765a1c537fdae71d5
+              url: http://cran.utstat.utoronto.ca/src/base/R-3/R-3.6.1.tar.gz
+            prereq_type: download
+          prereq_type: extract
+          configure: ["--with-x=no"]
+        build_type: autotools
+      - build_args:
+          package: devtools
+          # version: don't set, devtools is needed for versioned cran installs
+        build_type: cran
+        scan_dirs: true
+  system_depends:
+    - name: libcurl4-openssl-dev
+    - name: libbz2-dev
+    - name: libncurses5-dev
+    - name: libreadline-dev
+      permitted_os: ["Ubuntu18.04"]
+    - name: libreadline6-dev
+      permitted_os: ["Debian8.11"]
+    - name: liblzma-dev
+    - name: libpcre3-dev
+    - name: gfortran
+      required_at: build
+    - name: libgfortran-7-dev
+      permitted_os: ["Ubuntu18.04"]
+    - name: libgfortran-4.9-dev
+      permitted_os: ["Debian8.11"]
+
+# sequenza-scripts/2.1.2
+- name: sequenza-scripts
+  version: 2.1.2
+  build_type: custom
+  build_args:
+    prereq_args:
+      prereq_args:
+        sha256: aec68d6f47d3084a65ef5accbb12c8e70eeffb35ae04b371413cdf8323e34f42
+        url: https://github.com/oicr-gsi/sequenza/archive/2.1.2.tar.gz
+      prereq_type: download
+    prereq_type: extract
+    steps:
+      - build_type: cran
+        build_args:
+          package: openxlsx
+      - build_type: copy
+        build_args:
+          from:
+            - Generate_plody_priors_table.R
+            - SequenzaPreProcess_v2.2.R
+            - SequenzaProcess_v2.2.R
+          to: bin/
+  depends:
+  - name: rstats
+    version: 3.6

recipes/sequenza_recipe.yaml

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+# rstats/3.6
+- name: rstats
+  version: 3.6
+  build_type: custom
+  build_args:
+    steps:
+      - build_args:
+          prereq_args:
+            prereq_args:
+              md5: f5003472d58a3d3765a1c537fdae71d5
+              url: http://cran.utstat.utoronto.ca/src/base/R-3/R-3.6.1.tar.gz
+            prereq_type: download
+          prereq_type: extract
+          configure: ["--with-x=no"]
+        build_type: autotools
+      - build_args:
+          package: devtools
+          # version: don't set, devtools is needed for versioned cran installs
+        build_type: cran
+        scan_dirs: true
+  system_depends:
+    - name: libcurl4-openssl-dev
+    - name: libbz2-dev
+    - name: libncurses5-dev
+    - name: libreadline-dev
+      permitted_os: ["Ubuntu18.04"]
+    - name: libreadline6-dev
+      permitted_os: ["Debian8.11"]
+    - name: liblzma-dev
+    - name: libpcre3-dev
+    - name: gfortran
+      required_at: build
+    - name: libgfortran-7-dev
+      permitted_os: ["Ubuntu18.04"]
+    - name: libgfortran-4.9-dev
+      permitted_os: ["Debian8.11"]
+
+# bioconductor/3.8-rstats3.6
+- name: bioconductor
+  version: 3.8-rstats3.6
+  build_type: cran
+  build_args:
+    package: BiocManager
+    version: 1.30.4
+  depends:
+  - name: rstats
+    version: 3.6
+
+# sequenza/2.1.2
+- name: sequenza
+  version: 2.1.2
+  build_type: custom
+  build_args:
+    steps:
+      - build_type: bioc
+        build_args:
+          package: copynumber
+      - build_type: cran
+        build_args:
+          package: optparse
+      - build_type: cran
+        build_args:
+          package: sequenza
+          version: 2.1.2
+  depends:
+    - name: rstats
+      version: 3.6
+    - name: bioconductor
+      version: 3.8-rstats3.6
+      required_at: build
+
+# sequenza-scripts/2.1.2
+- name: sequenza-scripts
+  version: 2.1.2
+  build_type: custom
+  build_args:
+    prereq_args:
+      prereq_args:
+        sha256: 493b8ce6ae2397fbbc8f946a76cb5903e37ba224e9dfae0531f9d0f82ba86e93
+        url: https://github.com/oicr-gsi/sequenza/archive/v1.1.tar.gz
+      prereq_type: download
+    prereq_type: extract
+    steps:
+      - build_type: cran
+        build_args:
+          package: openxlsx
+      - build_type: copy
+        build_args:
+          from:
+            - Generate_plody_priors_table.R
+            - SequenzaPreProcess_v2.2.R
+            - SequenzaProcess_v2.2.R
+          to: bin/
+  depends:
+  - name: rstats
+    version: 3.6
+
+# sequenza-res/2.1.2
+- name: sequenza-res
+  version: 2.1.2
+  build_type: custom
+  build_args:
+    prereq_type: download
+    prereq_args:
+      sha256: b6604cf111849db6997c4ab0fc618f233fd63fc87a6381491470dfa6b1243bdc
+      url: http://api.gdc.cancer.gov/data/dea893cd-9189-4091-9611-e761a1d31ebe
+    steps:
+      - command: [ "Rscript", "{sequenza-scripts_root}/bin/Generate_plody_priors_table.R", "download" ]
+      - command: [ "cp", "PANCAN_ASCAT_ploidy_prob.Rdata", "{output_dir}/" ]
+  depends:
+    - name: sequenza-scripts
+      version: 2.1.2
+      required_at: build
+    - name: rstats
+      version: 3.6
+      required_at: build