Nextflow initital implementation for containerization

Author: Robert Patton

.dockerignore

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+# Directories
+.git/
+.gitignore
+results/
+logs/
+work/
+.nextflow/
+.nextflow.log*
+.DS_Store
+
+# Snakemake specific
+.snakemake/
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+*.egg-info/
+
+# Documentation and misc
+*.md
+!README.md
+misc/
+plotting/
+
+# Large data files
+*.bam
+*.bam.bai
+*.npz
+*.tsv
+*.bed
+*.fa
+*.fasta
+*.fai
+
+# Config files (will be mounted at runtime)
+config/samples.yaml
+config/cluster_slurm.yaml

.github/workflows/docker-build.yml

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+name: Build and Push Docker Container
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - 'v*'
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+env:
+  REGISTRY: docker.io
+  IMAGE_NAME: triton
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to Docker Hub
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ secrets.DOCKERHUB_USERNAME }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=raw,value=latest,enable={{is_default_branch}}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Generate Singularity recipe
+        if: github.event_name != 'pull_request'
+        run: |
+          echo "Bootstrap: docker" > Singularity.def
+          echo "From: ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.IMAGE_NAME }}:latest" >> Singularity.def
+          echo "" >> Singularity.def
+          echo "%help" >> Singularity.def
+          echo "    Triton - cfDNA fragmentomics and nucleosome analysis pipeline" >> Singularity.def
+          echo "    See https://github.com/${{ github.repository }} for more information" >> Singularity.def
+
+      - name: Upload Singularity recipe
+        if: github.event_name != 'pull_request'
+        uses: actions/upload-artifact@v4
+        with:
+          name: singularity-recipe
+          path: Singularity.def

.gitignore

@@ -1,13 +1,3 @@
-# local
-panel_info/GTRD_F1000_BackgroundPanel.npz
-panel_info/MANE.GRCh38.v1.3_TranscriptBodies_BackgroundPanel.npz
-panel_info/MANE.GRCh38.v1.3_TSS_BackgroundPanel.npz
-panel_gb/
-panel_tss/
-panel_info/results/*.npz
-panel_info/logs/cluster/*.out
-
-# Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class