merge-bridge

#!/bin/bash

set -e

CONNECT_USER="$1"
RUN_ID="$2"
RUN_DIR="$3"
BASE_NAME="$4"

START_DIR=`pwd`

if [ -e /stash2/user/$CONNECT_USER/public/$RUN_ID/level-2 ]; then
    cd /stash2/user/$CONNECT_USER/public/$RUN_ID/level-2
else
    cd $HOME/workflows/$RUN_ID/data
fi

for DIR in `ls -d $BASE_NAME-*`; do
    cd $DIR
    cp $BASE_NAME-*-merged.bam $START_DIR/
    cd ..
done