new file: bcbio.prepare_family1.sh

bcbio.prepare_family1.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+#prepare family for bcbio run when input files are family_sample.bam or family_sample_1/2.fq.gz
+
+family=$1
+
+cd $family
+
+cp ~/cre/bcbio.sample_sheet_header.csv $family.csv
+
+cd input
+
+ls | sed s/.bam// | sed s/.bai// | sed s/"_1.fq.gz"// | sed s/"_2.fq.gz"// | sort | uniq > ../samples.txt
+
+
+cd ..
+
+while read sample
+do
+    echo $sample","$sample","$family",,," >> $family.csv
+done < samples.txt
+
+bcbio_nextgen.py -w template ~/cre/bcbio.templates.exome.yaml $family.csv input/*
+
+mkdir config
+mkdir work
+
+cp $family/config/$family.yaml config
+
+cd ..
+
+