toggle functionality removed?

[jpsmith5]

Did the toggle function get removed?

In testing, it no longer seems to be recognized. In this case, a column in the sample annotation file named toggle, with entries of either 0 or 1.

[stolarczyk]

yes, I sort of unintentionally removed it because this came to my radar: pepkit/peppy#338

Current select samples functionality

select samples:
  This group of arguments lets you specify samples to use by exclusion OR
  inclusion of the samples attribute values.

  --selector-attribute SELECTOR_ATTRIBUTE
                        Specify the attribute for samples exclusion OR
                        inclusion
  --selector-exclude [SELECTOR_EXCLUDE [SELECTOR_EXCLUDE ...]]
                        Operate only on samples that either lack this
                        attribute value or for which this value is not in this
                        collection.
  --selector-include [SELECTOR_INCLUDE [SELECTOR_INCLUDE ...]]
                        Operate only on samples associated with these
                        attribute values; if not provided, all samples are
                        used.

is less flexible than toggle, but the new one could replace both in a nicer way.

what do you think @nsheff @jpsmith5 , do we bring toggle back or implement sample_filters? I think I like the latter a bit more.

[nsheff]

dunno... the toggle idea is nice in a way because it persists. but that's also the problem with it... it requires a change to the sample sheet, which we should try to avoid...

[stolarczyk]

in fact toggle sample attribute can an implied/derived/appended one (similar to pipeline_interface). This is probably how sample_filters woud work?

We could also keep the old toggle functionality and just follow the pipeline_interface example:

1. make toggle a special attr
2. allow to change it in looper:toggle_key