Hey people...thought this might be useful to someone when compiling the QC/run info that Illumina requests for a MiSeq run.
Example command is...
Code:
#!/bin/sh NASLOCATION=/Volumes/sequencing/output RUNDIR=$1 SOURCE=$NASLOCATION/$RUNDIR DEST=$2 TARGET=$2/$RUNDIR mkdir -p $TARGET/Thumbnail_Images/L001/ cp -R $SOURCE/InterOp $TARGET cp $SOURCE/RunInfo.xml $TARGET cp $SOURCE/runParameters.xml $TARGET cp $SOURCE/SampleSheet.csv $TARGET cp -R $SOURCE/Thumbnail_Images/L001/C1.1 $TARGET/Thumbnail_Images/L001/ cp -R $SOURCE/Thumbnail_Images/L001/C10.1 $TARGET/Thumbnail_Images/L001/ cp -R $SOURCE/Thumbnail_Images/L001/C100.1 $TARGET/Thumbnail_Images/L001/ cp -R $SOURCE/Thumbnail_Images/L001/C158.1 $TARGET/Thumbnail_Images/L001/ cp -R $SOURCE/Thumbnail_Images/L001/C168.1 $TARGET/Thumbnail_Images/L001/ cp -R $SOURCE/Thumbnail_Images/L001/C258.1 $TARGET/Thumbnail_Images/L001/ ZIPFILE=`basename $TARGET` zip -r $TARGET/$ZIPFILE $TARGET
Code:
get-crappy-miseq-run <RUNDIR> <DESTDIR>