Snakemake结合Singularity运行报错：未终止的引号字符串

Let's break down the two key problems you're facing and walk through actionable fixes:

1. Resolve the "unterminated quoted string" syntax error #

This error is almost certainly a bug in the Singularity macOS beta version you're using (3.3.0-rc.1), which has known issues parsing multi-line shell scripts from Snakemake. Try these fixes:

• Collapse multi-line shell commands into a single line: Replace the triple-quote multi-line shell script with a single line using && to chain commands. For your minimal example:

  rule counts:
      output: "output.txt"
      container: "docker://marcusczi/cellranger_clean"
      shell: "cellranger count --help && echo \"hurray!\" > {output}"
  

• Force bash instead of sh: Explicitly call bash inside the container to avoid sh's strict parsing rules. Modify your shell block like this:

  shell: """
      bash -c 'cellranger count --help; echo "hurray!" > {output}'
  """
  

• Upgrade Singularity (or switch to Docker): The 3.3.0 beta is unstable. If possible, switch to a stable Singularity release for macOS, or use Snakemake's --use-docker flag directly (since you're on macOS, Docker Desktop is a more mature option than Singularity's beta).

2. Fix Cellranger's false "disk space insufficient" error #

Cellranger's disk space check often misbehaves in Singularity containers on macOS due to how system partitions are mounted. Try these workarounds:

• Specify a custom temporary directory: Cellranger defaults to /tmp, which may be a small mounted partition in the container. Override it with a directory on your local large drive using the --tmpdir flag:

  shell: """
      cellranger count --id={wildcards.sample} --transcriptome={params.transcriptome} --fastqs={params.indir} --sample={params.name} --tmpdir /path/to/your/local/large/tmp
      mkdir -p {params.outdir}
      mv ./{wildcards.sample}/ {params.outdir}
  """
  

• Bind a local temp dir to the container: Add Singularity bind arguments to map your local temp space to the container's /tmp:
  Run Snakemake with:

  snakemake -j1 --use-singularity --singularity-args "--bind /your/local/large/tmp:/tmp"
  

Quick Debugging Checks #

• Test the container directly: Run the Singularity command outside Snakemake to isolate issues:

  singularity run docker://marcusczi/cellranger_clean cellranger count --help
  

  If this fails, the problem is with Singularity/container compatibility, not your Snakemake rule.
• Verify environment variables: Add env to your shell block to confirm variables like INDEX and OUTDIR are properly passed into the container:

  shell: """
      env
      cellranger count --id={wildcards.sample} --transcriptome={params.transcriptome} ...
  """
  

内容的提问来源于stack exchange，提问作者compuTE