Add in index file for azure

.devcontainer/Dockerfile

@@ -0,0 +1,20 @@
+# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.245.2/containers/python-3-anaconda/.devcontainer/base.Dockerfile
+
+FROM mcr.microsoft.com/vscode/devcontainers/anaconda:0-3
+
+# [Choice] Node.js version: none, lts/*, 16, 14, 12, 10
+ARG NODE_VERSION="none"
+RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# Copy environment.yml (if found) to a temp location so we update the environment. Also
+# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
+COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
+RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
+ && rm -rf /tmp/conda-tmp
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+# && apt-get -y install --no-install-recommends <your-package-list-here>
+
+RUN conda install -y -c conda-forge miniwdl
+RUN conda install -y -c conda-forge cromwell

.devcontainer/add-notice.sh

@@ -0,0 +1,19 @@
+# Display a notice when not running in GitHub Codespaces
+
+cat << 'EOF' > /usr/local/etc/vscode-dev-containers/conda-notice.txt
+When using "conda" from outside of GitHub Codespaces, note the Anaconda repository 
+contains restrictions on commercial use that may impact certain organizations. See
+https://aka.ms/vscode-remote/conda/anaconda
+
+EOF
+
+notice_script="$(cat << 'EOF'
+if [ -t 1 ] && [ "${IGNORE_NOTICE}" != "true" ] && [ "${TERM_PROGRAM}" = "vscode" ] && [ "${CODESPACES}" != "true" ] && [ ! -f "$HOME/.config/vscode-dev-containers/conda-notice-already-displayed" ]; then
+ cat "/usr/local/etc/vscode-dev-containers/conda-notice.txt"
+ mkdir -p "$HOME/.config/vscode-dev-containers"
+ ((sleep 10s; touch "$HOME/.config/vscode-dev-containers/conda-notice-already-displayed") &)
+fi
+EOF
+)"
+
+echo "${notice_script}" | tee -a /etc/bash.bashrc >> /etc/zsh/zshrc

.devcontainer/devcontainer.json

@@ -0,0 +1,50 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.2/containers/python-3-anaconda
+{
+ "name": "Anaconda (Python 3)",
+ "build": { 
+ "context": "..",
+ "dockerfile": "Dockerfile",
+ "args": {
+ "NODE_VERSION": "lts/*"
+ }
+ },
+
+ // Configure tool-specific properties.
+ "customizations": {
+ // Configure properties specific to VS Code.
+ "vscode": {
+ // Set *default* container specific settings.json values on container create.
+ "settings": { 
+ "python.defaultInterpreterPath": "/opt/conda/bin/python",
+ "python.linting.enabled": true,
+ "python.linting.pylintEnabled": true,
+ "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+ "python.formatting.yapfPath": "/opt/conda/bin/yapf",
+ "python.linting.flake8Path": "/opt/conda/bin/flake8",
+ "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+ "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+ "python.linting.pylintPath": "/opt/conda/bin/pylint"
+ },
+
+ // Add the IDs of extensions you want installed when the container is created.
+ "extensions": [
+ "ms-python.python",
+ "ms-python.vscode-pylance"
+ ]
+ }
+ },
+
+ // Use 'forwardPorts' to make a list of ports inside the container available locally.
+ // "forwardPorts": [],
+
+ // Use 'postCreateCommand' to run commands after the container is created.
+ // "postCreateCommand": "python --version",
+
+ // Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+ "remoteUser": "vscode",
+ "features": {
+ "ghcr.io/devcontainers/features/conda:1": {},
+ }
+}
+

.devcontainer/noop.txt

@@ -0,0 +1,4 @@
+
+This file copied into the container along with environment.yml* from the parent
+folder. This file is included to prevents the Dockerfile COPY instruction from 
+failing if no environment.yml is found.

pipelines/skylab/scATAC/scATAC.wdl

@@ -38,6 +38,7 @@ workflow scATAC {
  call SnapPre {
  input:
  input_bam = AlignPairedEnd.aligned_bam,
+ input_bam_index = AlignPairedEnd.aligned_bam_index,
  output_snap_basename = input_id + '.snap',
  genome_name = genome_name,
  input_reference = input_reference,
@@ -129,6 +130,7 @@ task AlignPairedEnd {
 
  output {
  File aligned_bam = output_bam
+ File aligned_bam_index = output_bam + ".bai"
  }
 
  runtime {
@@ -144,6 +146,7 @@ task AlignPairedEnd {
 task SnapPre {
  input {
  File input_bam
+ File input_bam_index
  String output_snap_basename
  String genome_name
  String genome_size_file = "genome/chrom.sizes"
@@ -157,6 +160,7 @@ task SnapPre {
 
  parameter_meta {
  input_bam: "input bam file"
+ input_bam_index: "input bam index file"
  output_snap_basename: "prefix name of the output bam file"
  genome_name: "name of the genome, currently not parsed but saved in output"
  genome_size_file: "name of the chrom.sizes file after unpacking of the genome reference"