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For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues on Github.
Using wdl when output filenames depend on input filenames
Redmar_van_den_Berg
Member ✭✭
Hi all,
I was wondering if there is a way to use wdl with programs that do not allow users to specify an output file.
We use a couple of bash commands to generate all the required index files for our analysis, and right now we have to manually include all index files in the .json file.
$ file=NC_011083.fasta
$ dict_file=${file%fasta}dict
$ picard-tools CreateSequenceDictionary R=$file O=$dict_file
$ samtools faidx $file
$ bwa index $file
Generated index files:
NC_011083.dict NC_011083.fasta.amb NC_011083.fasta.bwt NC_011083.fasta.pac NC_011083.fasta NC_011083.fasta.ann NC_011083.fasta.fai NC_011083.fasta.sa
NC_011083.dict gives the problem, since it wants to replace the extension, instead of just adding to it. Replacing the extension is of course the default behavior of many programs, how can we deal with this when using WDL?
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Answers
You can use the
sub()function to replace extensions. I went into a bit more detail on it here. We do use this function in our pipeline to help with replacing file extensions.