Merge pull request #2 from Sage-Bionetworks-Workflows/main

add old updates

.github/workflows/docker.yml

@@ -0,0 +1,94 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+#  schedule:
+#    - cron: '40 17 * * *'
+  push:
+    branches: [ "main" ]
+    # Publish semver tags as releases.
+    tags: [ 'v*.*.*' ]
+  workflow_dispatch:
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@v3
+        with:
+          cosign-release: 'v2.1.1'
+
+      # Workaround: https://github.com/docker/build-push-action/issues/461
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@v2
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v2
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v4
+        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
+
+
+      # Sign the resulting Docker image digest except on PRs.
+      # This will only write to the public Rekor transparency log when the Docker
+      # repository is public to avoid leaking data.  If you would like to publish
+      # transparency data even for private images, pass --force to cosign below.
+      # https://github.com/sigstore/cosign
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        # This step uses the identity token to provision an ephemeral certificate
+        # against the sigstore community Fulcio instance.
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

Dockerfile

@@ -14,20 +14,25 @@ ENV PATH=/root/miniconda3/bin:$PATH
 # Create conda environment 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH=/root/miniconda3/envs/vcf2maf/bin:$PATH
+ENV PATH=/root/miniconda3/envs/vep/bin:$PATH
 
 # rsync
 RUN yum install -y rsync \
     tar \
+    procps \
     perl \
     which
 
 # Install vcf2maf
-RUN bash -c 'export VCF2MAF_URL=`curl -sL https://api.github.com/repos/nf-osi/vcf2maf/releases | grep -m1 tarball_url | cut -d\" -f4`; curl -L -o nf-osi-vcf2maf.tar.gz $VCF2MAF_URL; tar -zxf nf-osi-vcf2maf.tar.gz; cd nf-osi-vcf2maf-*'
+RUN curl -s -L -o vcf2maf.tar.gz https://github.com/Sage-Bionetworks-Workflows/vcf2maf/archive/refs/tags/107.1.tar.gz \
+  && tar -zxf vcf2maf.tar.gz \
+  && rm vcf2maf.tar.gz \
+  && mv $(find . -maxdepth 1 -type d -name '*vcf2maf*') vcf2maf \
+  && chmod a+x vcf2maf/*.pl \
+  && ln -sr vcf2maf/*.pl /usr/local/bin/
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name vcf2maf > vcf2maf.yml
+RUN conda env export --name vep > vep.yml
 RUN conda init bash
 
 RUN mkdir /workdir
-

README.md

@@ -49,3 +49,47 @@ done
 
 
 ```
+
+## Adding support for `--af_gnomadg`
+
+### Original command
+
+```console
+docker run \
+	-v $HOME/data:/work/:rw -v /dev/shm/:/ref/:ro \
+	nfosi/vcf2maf:latest \
+	perl nf-osi-vcf2maf-1b34293/vcf2maf.pl --input-vcf /work/test-small.vcf \
+	--output-maf /work/test-small.maf --vep-data /ref/vep \
+	--ref-fasta /ref/fasta/Homo_sapiens_assembly38.fasta \
+	--vep-path /root/miniconda3/envs/vcf2maf/bin --ncbi-build GRCh38
+```
+
+### Using vcf2maf.sh
+
+This shell script adds support for `--af_gnomadg`
+
+```console
+docker run \
+	-v $HOME/data:/work/:rw -v /dev/shm/:/ref/:ro \
+	-v $HOME/vcf2maf-wf/:/src/:ro \
+	nfosi/vcf2maf:latest \
+	bash /src/vcf2maf.sh --input-vcf /work/test-small.vcf \
+	--output-maf /work/test-small.maf --vep-data /ref/vep \
+	--ref-fasta /ref/fasta/Homo_sapiens_assembly38.fasta \
+	--vep-path /root/miniconda3/envs/vcf2maf/bin --ncbi-build GRCh38
+```
+
+### Using vcf2maf-gnomad-genomes
+
+This uses a forked version of vcf2maf
+
+```console
+docker run \
+	-v $HOME/data:/work/:rw -v /dev/shm/:/ref/:ro \
+	sagebionetworks/vcf2maf:gnomad-genomes \
+	vcf2maf.pl --input-vcf /work/test-small.vcf \
+	--output-maf /work/test-small.maf --vep-data /ref/vep \
+	--ref-fasta /ref/fasta/Homo_sapiens_assembly38.fasta \
+	--vep-path /root/miniconda3/envs/vep/bin --ncbi-build GRCh38
+```
+

environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 # conda env create -f environment.yml
-name: vcf2maf
+name: vep
 channels:
   - conda-forge
   - bioconda