For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues on Github.
read_tsv() with a path to Google Bucket as an argument
I use the read_tsv() function to read an Array[Array[String]] from a .tsv file located in Google Storage bucket. This how the related part of our WDL script looks like:
File inputSamplesFile Array[Array[String]] inputSamples = read_tsv(inputSamplesFile)
It works fine in Firecloud, where the inputSamplesFile is passed as a workspace attribute and then as an input parameter to a method. But when my colleague tried to use Cromwell JES and the path to the file was written in the JSON input file, here is what happened:
java.lang.IllegalArgumentException: Could not find suitable filesystem among Default to parse gs://bucket-name/folder-name/file-name.tsv
If the same .tsv file is placed next to the Cromwell jar and the path to it is written in the JSON input file, all is working well. However, we would really like to be able to place the .tsv to Google Cloud Storage and use it with Cromwell JES. So, my questions are:
1) What might be causing the exception?
2) How can it be fixed?