new idea: sample_filters

[nsheff]

the sample_filters section lets you filter which samples are included.
it would behave like imply, sort of, but instead of adding new attributes, takes some samples out of consideration.

[stolarczyk]

isn't that exactly what selector functionality does in looper?

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.

do you suggest to move this functionality to peppy?

[nsheff]

yes that is a great way to put it!

maybe not worth thinking about. what do you think? this is not high priority...

[nsheff]

it could work like this:

project_modifiers:
  filter:
    - attribute: protocol
      include: ["ATAC-seq"]
      exclude: ["RNA-seq"]

for each attribute, you have to have either an include, or an exclude, or both.
if multiple values are listed under 'include/exclude', it ORs them.
if multiple attributes are listed, it ANDs them? Or, disallow multiple attributes.

looper selectors could then just offer a CLI interface to override this.