- runner.Args = append([]string{"vcf2fasta",
- "-local=true",
- "-ref", cmd.refFile, fmt.Sprintf("-mask=%v", cmd.mask),
- "-genome", cmd.genomeFile,
- "-gvcf-regions.py", "/gvcf_regions.py",
- "-output-dir", "/mnt/output"}, inputs...)
- var output string
- output, err = runner.Run()
+ var outputs []string
+ outputs, err = cmd.batchArgs.RunBatches(context.Background(), func(ctx context.Context, batch int) (string, error) {
+ runner := runner
+ if cmd.mask {
+ runner.RAM += int64(cmd.vcpus) << 31
+ }
+ runner.Args = []string{"vcf2fasta",
+ "-local=true",
+ "-ref", cmd.refFile, fmt.Sprintf("-mask=%v", cmd.mask),
+ "-genome", cmd.genomeFile,
+ "-gvcf-regions.py", "/gvcf_regions.py",
+ "-gvcf-type", cmd.gvcfType,
+ "-output-dir", "/mnt/output",
+ }
+ runner.Args = append(runner.Args, cmd.batchArgs.Args(batch)...)
+ runner.Args = append(runner.Args, inputs...)
+ log.Printf("batch %d: %v", batch, runner.Args)
+ return runner.RunContext(ctx)
+ })