{
  "name": "NGS tools sample",
  "summary": "Tiny FASTQ through fastqc + samtools",
  "containers": [
    "ngs-tools/2026.09"
  ],
  "steps": [
    {
      "id": "s1",
      "kind": "slurm-cpu",
      "name": "ngs",
      "script": "jobs/s1.sh",
      "after": [],
      "container": "ngs-tools/2026.09",
      "use_slurm": false,
      "copies": [],
      "shape": {
        "cpus": 2,
        "mem": "4G",
        "nodes": 1
      }
    }
  ],
  "files": {
    "jobs/s1.sh": "#!/bin/bash\nset -euo pipefail\nprintf '@r1\\nACGTACGTACGTACGT\\n+\\nIIIIIIIIIIIIIIII\\n' > reads.fq\napptainer exec /tmp/image.sif fastqc reads.fq\napptainer exec /tmp/image.sif samtools fqidx reads.fq\nls -l reads_fastqc.html reads.fq.fai\n"
  },
  "spans": []
}