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QC.wdl has invalid escape sequences #61

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jdidion opened this issue Jun 22, 2021 · 1 comment
Open

QC.wdl has invalid escape sequences #61

jdidion opened this issue Jun 22, 2021 · 1 comment

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@jdidion
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jdidion commented Jun 22, 2021

At line 35, the string "(\.fq)?(\.fastq)?(\.gz)?" is invalid, since \. is not a valid WDL escape sequence. The back-slashes need to be "double-escaped", i.e. "(\\.fq)?(\\.fastq)?(\\.gz)?". This is stated explicitly in the 1.1 spec under the sub function. Unfortunately it is not explicit in 1.0, but it is implied by the example used for sub.

@rhpvorderman
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Thank you for pointing this out.

This is due to our workflows being tested on Cromwell. Cromwell used to have the 'correct' behavior then it switched suddenly when a new version was released. I made a PR to make sure regular expressions are of a fixed format and should not rely on the implementation in the execution engine. Unfortunately this means that every 1.0 and prior version of WDL essentially has no 'valid escape sequences' because these are not defined.

I will check if newer versions handle this correctly. Currently cromwell has no explicit 1.1 support unfortunately. And we rely heavily on cromwell in our institute. Once cromwell is ready we will switch to 1.1 as soon as possible and fix this issue.

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