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Write results to cwl.output.json to bypass size restrictions

Matthijs van der Wild requested to merge hotfix_filter_ms_group into master

This MR modifies the way LINC collects the output in the filter_ms_group step. The output is written to cwl.output.json, which is then parsed as part of the collection of the outputs. This the loadContents field to circumvent size restrictions.

Solves #63 (closed).

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