Feature/workflow

.github/workflows/main.yml

@@ -1,15 +1,98 @@
-name: Test container build
+name: Build, Lint, and Test
 
 on:
   push:
     branches:
       - master
   pull_request:
-    branches_ignore: []
+    branches-ignore: []
+
+env:
+  DOCKER_TAG_NAME: snakemake-tutorial
 
 jobs:
+  docker-build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - name: Setup Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Lint Dockerfile
+        uses: hadolint/hadolint-action@v3.1.0
+        with:
+          dockerfile: Dockerfile
+          no-fail: true
+
+      - name: Build Docker Image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: Dockerfile
+          tags: ${{ env.DOCKER_TAG_NAME }}
+          outputs: type=docker, dest=/tmp/${{ env.DOCKER_TAG_NAME }}.tar
+
+      - name: Upload Artifact
+        uses: actions/upload-artifact@v4
+        with: 
+          name: ${{ env.DOCKER_TAG_NAME }}
+          path: /tmp/${{ env.DOCKER_TAG_NAME }}.tar
+
+  lint:
+    runs-on: ubuntu-latest
+    needs: docker-build
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Lint Snakefile
+        uses: github/super-linter@v7
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: master
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+          VALIDATE_SNAKEMAKE_SNAKEFMT: true
+
+      - name: Download Artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: snakemake-tutorial
+          path: /tmp
+
+      - name: Load Docker Image
+        run: docker load -i /tmp/${{ env.DOCKER_TAG_NAME }}.tar
+
+      - name: DryRun Snakefile
+        run: docker run ${{ env.DOCKER_TAG_NAME }} snakemake --cores 1 --dryrun
+
   test:
     runs-on: ubuntu-latest
+    needs: docker-build
     steps:
-    - uses: actions/checkout@master
-    - run: docker build .
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - name: Setup Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Download Artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: ${{ env.DOCKER_TAG_NAME }}
+          path: /tmp
+
+      - name: Load Docker Image
+        run: docker load -i /tmp/${{env.DOCKER_TAG_NAME}}.tar
+
+      - name: Run Tests
+        run: docker run -v $(pwd):/work -w /work ${{env.DOCKER_TAG_NAME}} \
+            conda run -n ${{env.DOCKER_TAG_NAME}} -tutorial snakemake --cores 1
+

.gitignore

@@ -0,0 +1,5 @@
+calls
+plots
+sorted_reads
+mapped_reads
+.snakemake

Dockerfile

@@ -1,6 +1,6 @@
 FROM snakemake/snakemake:stable
 ADD environment.yaml .
 RUN conda create -n snakemake-tutorial --clone snakemake; \
     conda env update -n snakemake-tutorial -f environment.yaml;
 RUN mkdir -p /tmp/conda
-ENV CONDA_PKGS_DIRS /tmp/conda
+ENV CONDA_PKGS_DIRS=/tmp/conda

workflow/Snakefile

@@ -0,0 +1,56 @@
+SAMPLES = ["A", "B"]
+
+
+rule all:
+    input:
+        "plots/quals.svg",
+
+
+rule bwa_map:
+    input:
+        "data/genome.fa",
+        "data/samples/{sample}.fastq",
+    output:
+        "mapped_reads/{sample}.bam",
+    shell:
+        "bwa mem {input} | samtools view -Sb - > {output}"
+
+
+rule samtools_sort:
+    input:
+        "mapped_reads/{sample}.bam",
+    output:
+        "sorted_reads/{sample}.bam",
+    shell:
+        "samtools sort -T sorted_reads/{wildcards.sample} "
+        "-O bam {input} > {output}"
+
+
+rule samtools_index:
+    input:
+        "sorted_reads/{sample}.bam",
+    output:
+        "sorted_reads/{sample}.bam.bai",
+    shell:
+        "samtools index {input}"
+
+
+rule bcftools_call:
+    input:
+        fa="data/genome.fa",
+        bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES),
+    output:
+        "calls/all.vcf",
+    shell:
+        "bcftools mpileup -f {input.fa} {input.bam} | "
+        "bcftools call -mv - > {output}"
+
+
+rule plot_quals:
+    input:
+        "calls/all.vcf",
+    output:
+        "plots/quals.svg",
+    script:
+        "scripts/plot-quals.py"

workflow/scripts/plot-quals.py

@@ -0,0 +1,9 @@
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+from pysam import VariantFile
+
+quals = [record.qual for record in VariantFile(snakemake.input[0])]
+plt.hist(quals)
+
+plt.savefig(snakemake.output[0])