checkProjectComplete.sh

[denriquez]

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 $usableName | cut -d '-' -f1-2`
        vcfACmergeTrack=$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 "-"

[denriquez]

Dang it! I forgot the code itself had backticks that threw off the format.

[PedalheadPHX]

Is it better to add the check to the start of the pipeline? Then error if this is the case?

Sent from a Handheld Device

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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[denriquez]

Yes, actually Ryan did talk about adding more validation steps which is definitely a good idea because of problems like this.