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122 issues in broadinstitute/wdl

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#124

Fix typo in SPEC.md

  • Opened by danbills Jul 20, 2017
  • 2 comments
#123

small typo in SPEC.md

It says: "Tasks define all their outputs as declarations at the top of the task definition." It should say: "Tasks define all their inputs as declarations at the top of the task definition." ...

#122

fixing typo in cross example

replacing incorrect use of crossProduct with cross

#121

Floor, Round and Ceil docs

#120

array slices

Very often I need to slice an array. For instance, in RNA-Seq experiments I have tsv files with first column as a condtion and all subsequent as GSM ids for samples. It would be useful to get all elements ...

#119

Take over Google's wdl_runner

This copies the code from https://github.com/googlegenomics/pipelines-api-examples/ and renames "wdl_runner" to "cromwell-on-google" to be more specific.

  • Opened by vdauwera Jun 28, 2017
  • 1 comment
#118

Discrepancies within WDL script in converting to CWL

We are converting the WDL scripts to CWL, and there seem to be some discrepancies regarding the correct way to format arguments within the command line with boolean values. While working on converting ...

#117

A contains style function for Array

This WDL forum post presents a use-case for why a contains style function on arrays could be very useful. It also reflects on the downsides of current workarounds in WDL. It would be helpful to have a ...

  • Opened by ruchim Jun 19, 2017
#116

quote command part option undocumented

In the spec, a command part option named quote is listed: https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#command-part-options However, although the spec goes on to have a subsection explaining ...

#115

true and false command part options function unclear (and example broken)

It appears that the command part options example for true and false given in the SPEC (https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#true-and-false) is broken. First of all, the parser does ...

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