rnaAlign.sh script has a bug

[tgenahmet]

The rnaAlign script has a bug (only matters when trying to re-run). Needs to be fixed. While trying to debug I also realized the code is way more complicated than it needs to be. rnaAlign script in medusa makes a lot more sense. My plan is to change pegasus-rnaAlign to be more like medusa-rnaAlign.

Here's the question: what are the differences in rnaAlign between medusa and pegasus that I may not be aware of?

@denriquez @awchrist @PedalheadPHX

[PedalheadPHX]

@tgenahmet @awchrist @denriquez

The biggest difference is that Pegasus: 1) Uses a newer version of STAR 2) It enforces that the RNA BAM now have RG tags just like we do on DNA.

As far as I remember those are the only differences. There maybe some different run settings related

[denriquez]

The rnaAlign script still has a bug that occurs when re-running it. This code did the trick (I used "git diff" so sorry about the formatting) for now:

index df9ec7c..4f483a1 100755 --- a/pegasus_rnaAlign.sh +++ b/pegasus_rnaAlign.sh @@ -198,7 +198,12 @@ do

fi

                                                    if [[ -e $ownDir.starPass || -e $ownDir.starFail || -e $ownDir.starInQueue ]] ; then
                                                            echo "### STAR already done, failed or inQueue"

• kitName=echo $configLine | cut -d= -f2 | cut -d, -f1
• samName=echo $configLine | cut -d= -f2 | cut -d, -f2
• assayID=echo $configLine | cut -d= -f2 | cut -d, -f3 unset mergeArray
• count=0
• skipGroup=0 continue fi

Let me know your thoughts. I haven't pushed yet.

[denriquez]

Ugghhh! Github changed the format. Here is the code again: if [[ -e $ownDir.starPass || -e $ownDir.starFail || -e $ownDir.starInQueue ]] ; then echo "### STAR already done, failed or inQueue" kitName=echo $configLine | cut -d= -f2 | cut -d, -f1 samName=echo $configLine | cut -d= -f2 | cut -d, -f2 assayID=echo $configLine | cut -d= -f2 | cut -d, -f3 unset mergeArray count=0 skipGroup=0 continue fi