Derek Ruths issues

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                                            Derek Ruths

Migrate file format to yml

enhancement

Output for a task should be cached

The output for a task should be saved such that it can be retrieved at a later time.

enhancement

Stack traces in code blocks don't reference the right pipeline or line numbers

The use of temporary files makes this a bit clunky, but possible to trace back to the original code block. But it would be better to transform the stack trace...

enhancement

In multi-line comment inside task, empty lines trigger a parse error

``` sh task1: ### Align the networks using the CGRAAL algorithm. http://bio-nets.doc.ic.ac.uk/C-GRAAL/ Basically, a common-neighbor model. ### code.sh: touch $PLN(empty_similarity.txt) ```

bug

When a task doesn't exist (but is specified), tasks should be suggested

enhancement

Support existing_file type - which will check and make sure the file exists.

enhancement