Open rekado opened 4 years ago
Hi @rekado,
I guess we can lower these requirements, they are defined in the settings file (https://github.com/BIMSBbioinfo/pigx_bsseq/blob/master/etc/settings.yaml.in#L101).
I just realized now that these memory and thread settings refer to samtools actually, however these settings should probably be as rule specific as possible and thus I need to add another section for the deduplication_se/_pe rules.
Probably we should also try some profiling to determine minimum memory requirement to achieve a acceptable pipeline runtime.
I tried upgrading the Guix package to 0.1.2 but ran into this error during the check phase:
...
Looking at the log file I see that I don't have enough memory:
Is this expected? Oh, wait: it is! The command looks like this:
... -m 12G...
. Why that much memory? Can we get by with less?Alternatively, can we disable this step for the test suite?