allow user to specify job name

[flass]

beautiful code project!

I could see there https://github.com/SamD28/arrayify/blob/b8b1d1418143e4191be02cce5eccb4b81d0eb45c/src/submission.rs#L59C29-L59C38
that the array job is named something generic. could you make an option that allows the user to specify at least a prefix for the job name? I think that would enable better tracking of what they do - imagine there is a wide adoption of the tool on the Sanger far, then (based on current code) all the farm jobs would suddenly be called arrayify_job_array.

Florent

[SamD28]

Agreed! It's a very small change too! :)

[SamD28]

./target/release/arrayify sub -h
Submit a job array from a CSV file or a directory

Usage: arrayify sub [OPTIONS] --command <COMMAND_TEMPLATE>

Options:
  -s, --csv <CSV_FILE>              Path to the CSV file containing job information
  -d, --dir <DIRECTORY>             Path to the directory containing input files
  -c, --command <COMMAND_TEMPLATE>  Command template using placeholders for CSV headers
  -p, --job_prefix <PREFIX>         prefix for job submission name i.e. prefix_job_array [default: arrayify]
  -l, --log <LOG_DIR>               Directory to store log files [default: logs]
  -m, --memory <MEMORY_GB>          Amount of memory per job in GB [default: 1]
  -t, --threads <THREADS>           Number of threads per job [default: 1]
  -b, --batch <BATCH_SIZE>          Number of jobs running concurrently (default: 20% of array) [default: auto]
  -q, --queue <QUEUE>               Bsub queue to submit to [default: normal]
  -h, --help                        Print help (see more with '--help')

Will deploy and run a quick test

[SamD28]

arrayify sub -p test -s manifest.csv -c "echo {ID}"
🚀 Job submission complete! ✅
🔖 Job ID is: 246659
📌 3 jobs submitted.
📝 Job commands logged in: logs/arrayify-2025-03-07-16-21.log
📂 Logs can be found in: logs
📡 Track with -
   arrayify check 246659

bjobs -w | grep 246659
246659[1] sd28    RUN   normal     farm22-pam-01 node-14-20  test_job_array[1] Mar  7 16:21
246659[2] sd28    PEND  normal     farm22-pam-01    -        test_job_array[2] Mar  7 16:21
246659[3] sd28    PEND  normal     farm22-pam-01    -        test_job_array[3] Mar  7 16:21

arrayify check still unaffected

arrayify check 246659
🚀 1 jobs are currently running!
⏳ 2 jobs are still pending!

[SamD28]

Unsure if it is better like this or just allow full control I don't really see a huge reason to enforce job_array other than maybe "tracking" arrayify runs?

[flass]

happy with that!