wdl-cwl-translator

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https://github.com/DataBiosphere/wdl-conformance-tests See #245 for an example

mr-c

Handle cases where the WDL workflow output contains exprs

3

Closes #200 @admi2u, can you check if this branch's code works for you? It produced the `blast.cwl` file in this branch/pull request. I am taking a look at the tests...

kinow

Example: https://github.com/common-workflow-lab/wdl-cwl-translator/blob/1fff15bd7b4e7f0bff540b01276881c1b00d1f39/wdl2cwl/tests/wdl_files/blast.wdl#L12 1. Synthesize a new step to compute a static value for each dynamic input, something like `_calc_{inputname}`: `_calc_Outfile` with a single output named `result` 2. Rewrite all references...

mr-c

Paper

1

JOSS paper issue #180

ntachukwu

Try a different module/package structure

6

It started over the week/holiday when I had a go at trying to write the conversion for WDL stdlib's `select_all` function. It didn't work for [other reasons](https://github.com/chanzuckerberg/miniwdl/issues/541), but I noticed...

kinow

Some WDL Maps are not handled

8

Currently, the WDL input compound type ```Map[]``` is not handled by the translator. (https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#mapp-y) ~~A workflow using Maps is given in this workflow (https://github.com/biowdl/tasks/blob/bc1bacf11498d2d30b85591cfccdcf71ef0966a5/star.wdl#L144)~~ edit by @mr-c , we now...

dinithiW

translate WDL's sub() as replaceAll() equivalent not replace()

4

From WDL [spec](https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md#string-substring-string-string): >this function replaces all non-overlapping occurrences of pattern in input by replace But I think what we have in the `get_expr_apply` is a call to `.replace()` which...

kinow

https://github.com/common-workflow-lab/wdl-cwl-translator/pull/173#discussion_r806035140

mr-c

JOSS Paper

1

@Th3nn3ss if you'd like to read about the Journal of Open Source Software: https://joss.theoj.org/ The publication process is really straightforward once an editor is assigned and whoever is the editor...

kinow

https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#arrayint-rangeint Example: https://github.com/broadinstitute/viral-ngs/blob/e144969e4c57060d53f38a4c3a270e8227feace1/pipes/WDL/workflows/tasks/tasks_ncbi.wdl#L67 advanced example with scatter: https://github.com/dnanexus/dxWDL/blob/0570b7a91b1a089432723e857f518658c0ca7cdc/test/draft2/var_type_change.wdl#L7

mr-c