add GitHub Actions build, modernizing docker image & WDL

.github/workflows/build.yml

@@ -0,0 +1,52 @@
+name: build
+on: [push, pull_request]
+
+jobs:
+
+  lint:
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/checkout@v2
+    - name: deps
+      run: |
+        sudo apt-get -qq update
+        sudo apt-get install -y clang-format cppcheck python3-pip
+        sudo pip3 install --system pre-commit
+    - name: pre-commit
+      run: pre-commit run --all-files
+
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/checkout@v2
+    - name: build
+      run: |
+        docker pull ubuntu:18.04
+        docker pull ubuntu:20.04
+        docker build --no-cache -t spvcf .
+    - name: inspect
+      run: |
+        docker run -v $(pwd):/mnt spvcf cp /usr/local/bin/spvcf /mnt
+        ldd spvcf
+        sha256sum spvcf
+    - name: upload exe
+      uses: actions/upload-artifact@v2
+      with:
+        name: spvcf
+        path: spvcf
+    - name: WDL test
+      run: |
+        pip3 install --upgrade miniwdl
+        miniwdl run test/test_spvcf.wdl vcf_gz=test/data/small.vcf.gz docker=spvcf:latest --verbose
+    - name: docker login ghcr.io
+      uses: docker/login-action@v1
+      with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+    - name: push image
+      run: |
+        REPO="ghcr.io/mlin/spvcf"
+        TAG="$(git describe --tags --always --dirty)"
+        docker tag spvcf:latest "${REPO}:${TAG}"
+        docker push "${REPO}:${TAG}"

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+repos:
+- repo: local
+  hooks:
+  - id: clang-format
+    name: clang-format
+    language: system
+    files: \.(c|cc|cxx|cpp|h|hpp|hxx)$
+    exclude: (json1|uint)\.c
+    verbose: true
+    entry: clang-format
+    args: [-i,'-style={IndentWidth: 4, ColumnLimit: 100, BreakStringLiterals: false, ReflowComments: false}']
+  - id: cppcheck
+    name: cppcheck
+    language: system
+    files: \.(c|cc|cxx|cpp|h|hpp|hxx)$
+    exclude: json1\.c
+    verbose: true
+    entry: cppcheck
+    args: [-q,--language=c++,--std=c++14]

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:18.04
+FROM ubuntu:18.04 AS builder
 ENV DEBIAN_FRONTEND noninteractive
 
 RUN apt-get -qq update && \
@@ -14,4 +14,12 @@ RUN make -j $(nproc) && make install
 ADD . /src
 WORKDIR /src
 RUN rm -f CMakeCache.txt && cmake -DCMAKE_BUILD_TYPE=Release /src && make clean && make -j$(nproc)
-CMD ctest -V
+RUN ctest -V
+
+
+FROM ubuntu:20.04
+RUN apt-get -qq update && \
+     apt-get -qq install -y --no-install-recommends --no-install-suggests \
+     tabix bcftools less
+COPY --from=builder /src/spvcf /usr/local/bin/spvcf
+CMD ["spvcf"]

spvcf.wdl

@@ -4,7 +4,7 @@ task spvcf_encode {
     input {
         File vcf_gz
         Boolean multithread = false
-        String release = "v1.1.0"
+        String docker = "ghcr.io/mlin/spvcf:v1.2.0"
         Int cpu = if multithread then 8 else 4
     }
 
@@ -15,10 +15,6 @@ task spvcf_encode {
     command <<<
         set -euxo pipefail
 
-        apt-get -qq update && apt-get install -y wget tabix
-        wget -nv https://github.com/mlin/spVCF/releases/download/~{release}/spvcf
-        chmod +x spvcf
-
         threads_arg=""
         if [ "~{multithread}" == "true" ]; then
             threads_arg="--threads 4"
@@ -27,11 +23,11 @@ task spvcf_encode {
         nm=$(basename "~{vcf_gz}" .vcf.gz)
         nm="${nm}.spvcf.gz"
         mkdir out
-        bgzip -dc "~{vcf_gz}" | ./spvcf encode $threads_arg | bgzip -@ 4 > "out/${nm}"
+        bgzip -dc "~{vcf_gz}" | spvcf encode $threads_arg | bgzip -@ 4 > "out/${nm}"
     >>>
 
     runtime {
-        docker: "ubuntu:20.04"
+        docker: docker
         cpu: cpu
         memory: "~{cpu} GB"
         disks: "local-disk ~{ceil(size(vcf_gz,'GB'))} SSD"
@@ -45,7 +41,7 @@ task spvcf_encode {
 task spvcf_decode {
     input {
         File spvcf_gz
-        String release = "v1.1.0"
+        String docker = "ghcr.io/mlin/spvcf:v1.2.0"
     }
 
     parameter_meta {
@@ -55,18 +51,14 @@ task spvcf_decode {
     command <<<
         set -euxo pipefail
 
-        apt-get -qq update && apt-get install -y wget tabix
-        wget -nv https://github.com/mlin/spVCF/releases/download/~{release}/spvcf
-        chmod +x spvcf
-
         nm=$(basename "~{spvcf_gz}" .spvcf.gz)
         nm="${nm}.vcf.gz"
         mkdir out
-        bgzip -dc "~{spvcf_gz}" | ./spvcf decode | bgzip -@ 4 > "out/${nm}"
+        bgzip -dc "~{spvcf_gz}" | spvcf decode | bgzip -@ 4 > "out/${nm}"
     >>>
 
     runtime {
-        docker: "ubuntu:20.04"
+        docker: docker
         cpu: 4
         memory: "4 GB"
         disks: "local-disk ~{10*ceil(size(spvcf_gz,'GB'))} SSD"
@@ -81,7 +73,7 @@ task spvcf_squeeze {
     input {
         File vcf_gz
         Boolean multithread = false
-        String release = "v1.1.0"
+        String docker = "ghcr.io/mlin/spvcf:v1.2.0"
         Int cpu = if multithread then 8 else 4
     }
 
@@ -92,10 +84,6 @@ task spvcf_squeeze {
     command <<<
         set -euxo pipefail
 
-        apt-get -qq update && apt-get install -y wget tabix
-        wget -nv https://github.com/mlin/spVCF/releases/download/~{release}/spvcf
-        chmod +x spvcf
-
         threads_arg=""
         if [ "~{multithread}" == "true" ]; then
             threads_arg="--threads 4"
@@ -104,11 +92,11 @@ task spvcf_squeeze {
         nm=$(basename "~{vcf_gz}" .vcf.gz)
         nm="${nm}.squeeze.vcf.gz"
         mkdir out
-        bgzip -dc "~{vcf_gz}" | ./spvcf squeeze $threads_arg | bgzip -@ 4 > "out/${nm}"
+        bgzip -dc "~{vcf_gz}" | spvcf squeeze $threads_arg | bgzip -@ 4 > "out/${nm}"
     >>>
 
     runtime {
-        docker: "ubuntu:20.04"
+        docker: docker
         cpu: cpu
         memory: "~{cpu} GB"
         disks: "local-disk ~{ceil(size(vcf_gz,'GB'))} SSD"