I have a line in my WDL command that looks like this
"#source /usr/local/run_OrientationBias_filter.sh ${ID} ${BAM} ${MAF} ${REFERENCE} ${DBSNP} ${CONTEXT} ${ALTALLELE} ${STUB} ${OUT} ;"
See that the entire line in the command is commented out.
Though the line is commented out when I tell my local cromwell to run the WDL I still get an error saying "Failing call: Could not find declaration for OUT" (see it's at the end of the line). I had JUST removed OUT from the INPUT list in the task and the INPUT list in the workflow. After I removed OUT from the commented line, cromwell had no issue.
It was for a moment confusing that the commented line caused a problem, but I soon realized that the comment is in the command-level but not a comment in the WDL (parsed) level.
It's somewhat of a contradiction to have to change a commented line to cause an error to go away. That contradiction is the root of the confusion and what I wonder if can be eliminated.
SO, my wonder is if cromwell parsing can NOT throw errors on lines that are commented in the command...cause that could avoid some confusions on some occasions.