Open denriquez opened 7 years ago
Dang it! I forgot the code itself had backticks that threw off the format.
Is it better to add the check to the start of the pipeline? Then error if this is the case?
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On Aug 5, 2017, at 20:00, denriquez notifications@github.com wrote:
There is a bug that occurs only when the normal/control sample name contains "-." This bug makes this script look for a non-existent vcfMergerAC (alleleCount version) pass file. The problem occurs in this section: usableName2=echo $usableName | cut -d '-' -f1-2vcfACmergeTrack=$runDir/vcfMerger/$usableName2/$usableName2 if [ ! -e $vcfACmergeTrack.vcfMergerACPass ] ; then echo "### vcfMerger alleleCountPass does not exist on allele output!" echo "### Missing file: $vcfACmergeTrack.vcfMergerACPass" ((missingvcfMergerAC++)) The naming convention is usually normal/control and tumor/affected separated with "-"
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Yes, actually Ryan did talk about adding more validation steps which is definitely a good idea because of problems like this.
There is a bug that occurs only when the normal/control sample name contains "-." This bug makes this script look for a non-existent vcfMergerAC (alleleCount version) pass file. The problem occurs in this section:
The naming convention is usually normal/control and tumor/affected separated with "-"