Detect when running under a non-interactive session and do not display progress bar

[hexylena]

It really fills up the stderr.txt

$ du -h *
32K     command
32K     error.json
32K     inputs.json
32K     slurm-23041630.out
32K     slurm_singularity.log.txt
216K    stderr.txt

The job died due to timeout, but I always start by looking in the stderr for relevant messages, here the signal to noise ratio is a bit low

(newlines inserted manually, less doesn't handle control characters)

Processing 392b181d6b_hg38.bam:  48%|████▊     | 63.3G/131G [59:04<1:31:36, 13.1MiB/s]^M
Processing 392b181d6b_hg38.bam:  48%|████▊     | 63.3G/131G [59:04<1:28:38, 13.6MiB/s]^M
Processing 392b181d6b_hg38.bam:  48%|████▊     | 63.3G/131G [59:04<1:26:01, 14.0MiB/s]^M
Processing 392b181d6b_hg38.bam:  49%|████▊     | 63.3G/131G [59:05<1:23:08, 14.5MiB/s]^M

It seems tqdm doesn't do this automatically and someone makes a community replacement but that seems.. suspect at best, so maybe it's possible to detect easily and just toggle it off in that case.

[rhpvorderman]

Yes. There needs to be a check if it is connected to a TTy or not. If not there should be no tqdm progress bar, but rather a percentage update like fastqc.
I will put this on the todo list.