For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues on Github.
Overzealous call caching
For our analysis, we use a input file with all our samples of format
samplename /path/to/forward_reads.fastq.gz /path/to/reverse_reads.fastq.gz. I wanted to add support for spaces in filenames, which does not work currently. So I made a folder with a space in the name and hardlinked the fastq files there.
mkdir path\ with\ space cd path\ with\ space ln /path/to/*.fastq.gz .
I then updated the input file to include
samplename /path with space/forward_reads.fastq.gz /path with space/reverse_reads.fastq.gz and ran the analysis with cromwell on this file.
To my surprise, the analysis completed successfully. However, when I look at the
cromwell-execution folder, there are not
inputs folders for any of the tasks, and when I look in the
script file I see the inputs refer to
/path/to/forward_reads.fastq.gz, instead of
/path with space/forward_reads.fastq.gz.
Is this the expected behaviour? I would expect cromwell to notice the sample input file has changed, which should invalidate all cached calls that inherit from that file. How can I make sure that cromwell doesn't re-use the results from an earlier version when I change the input file?