Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

Confusion over nested pairs

flehartyfleharty Member, Broadie, Dev ✭✭

Hello,

I'm trying to use a nested pair in WDL.
Array[File] bam_files
Array[File] bam_indices
Array[String] base_names
Array[Pair[File, File]] bam_index_pair = zip(bam_files, bam_indices)
Array[Pair[String, Pair[File, File]]] basename_bam_index_pair = zip(base_names, bam_index_pair)

In scatter block:
scatter (paired_data in basename_bam_index_pair) {
call CalculateCoverage {
input:
gatk_jar = gatk_jar,
bam_file = paired_data.right.left, // This is line 56 that I get the error message on.
bam_index = paired_data.right.right,
base_name = paired_data.left,
interval_list = interval_list,

The error I get is:
"message": "Unable to load namespace from workflow: ERROR: Expression will not evaluate (line 56, col 42):\n\n bam_file = paired_data.right.left,\n ^\n "

Any thoughts on how I can resolve this?

Thanks!
Mark

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Answers

  • flehartyfleharty Member, Broadie, Dev ✭✭

    @ChrisL This works. Thanks!

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