Fix find for issue #109. Bump Docker base image to 20.04 (#111)

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:18.04 as builder
+FROM ubuntu:20.04 as builder
 
 RUN apt-get update && \
     apt-get upgrade -y && \
@@ -90,7 +90,12 @@ RUN wget https://github.com/samtools/samtools/archive/0.1.17.tar.gz && \
 
 RUN SAMTOOLS="/tmp/samtools-0.1.17" cpanm --force -i Bio::DB::[email protected] && chown -R root:root /usr/local/.cpanm
 
-FROM ubuntu:18.04
+FROM ubuntu:20.04
+
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y libncursesw5 && \
+    rm -r /var/lib/apt/lists/*
 
 COPY --from=builder /opt/conda/bin/gfClient /opt/conda/bin/gfClient
 COPY --from=builder /opt/conda/bin/gfServer /opt/conda/bin/gfServer

src/scripts/Cicero.sh

@@ -334,10 +334,12 @@ parallel --joblog 02_Cicero.log $PARALLEL_ARG < cmds-02.sh
 #########################
 echo "Step 03 - $(date +'%Y.%m.%d %H:%M:%S') - Combine"
 {
-find $CICERO_DATADIR/$SAMPLE/*/ -type f -name 'unfiltered.fusion.txt' -exec cat {} \; | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.fusion.txt
-find $CICERO_DATADIR/$SAMPLE/*/ -type f -name 'unfiltered.internal.txt' -exec cat {} \; | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.internal.txt
+find $CICERO_DATADIR/$SAMPLE/ -mindepth 2 -type f -name 'unfiltered.fusion.txt' -exec cat {} \; | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.fusion.txt
+find $CICERO_DATADIR/$SAMPLE/ -mindepth 2 -type f -name 'unfiltered.internal.txt' -exec cat {} \; | sort -V -k 9,9 -k 10,10n -k 11,11n > $CICERO_DATADIR/$SAMPLE/unfiltered.internal.txt
 } 1> 03_Combine.out 2> 03_Combine.err
 
+wait
+
 ## QC
 if [ ! -s $CICERO_DATADIR/$SAMPLE/unfiltered.fusion.txt ]
 then