From 6cc144e577215cbec7bd5e053d170135a24b6f96 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Tue, 26 Nov 2019 20:17:20 +0000
Subject: [PATCH] Reads are merged/linked into per-project directories to avoid
sample id collisions for repeats.
---
prepare_bcbio_config.sh | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/prepare_bcbio_config.sh b/prepare_bcbio_config.sh
index 85cc757..e81baac 100755
--- a/prepare_bcbio_config.sh
+++ b/prepare_bcbio_config.sh
@@ -44,6 +44,9 @@ cd $PARAMS_DIR
# remove DOS newline characters if necessary
perl -pi -e 's/\r//' $PROJECT_ID.ped
+# create reads directory for project
+mkdir -p $READS_DIR/$PROJECT_ID
+
cat $DOWNLOAD_DIR/$PROJECT_ID/raw_data/*/file_list.tsv | \
perl $SCRIPTS/trio_whole_exome_create_parameter_files.pl \
--prefix ./$PROJECT_ID \
@@ -68,13 +71,13 @@ do
done
- bcbio_prepare_samples.py --out $READS_DIR --csv ${PROJECT_ID}_${FAMILY_ID}.csv
+ bcbio_prepare_samples.py --out $READS_DIR/$PROJECT_ID --csv ${PROJECT_ID}_${FAMILY_ID}.csv
mv ${PROJECT_ID}_${FAMILY_ID}-merged.csv ${PROJECT_ID}_${FAMILY_ID}.csv
BARE_FAMILY_ID=`echo $FAMILY_ID | cut -d '_' -f 2`
- bcbio_nextgen.py -w template $BCBIO_TEMPLATE ${PROJECT_ID}_${FAMILY_ID}.csv $READS_DIR/*_${BARE_FAMILY_ID}_R[12].fastq.gz
+ bcbio_nextgen.py -w template $BCBIO_TEMPLATE ${PROJECT_ID}_${FAMILY_ID}.csv $READS_DIR/$PROJECT_ID/*_${BARE_FAMILY_ID}_R[12].fastq.gz
mv ${PROJECT_ID}_${FAMILY_ID}/config/${PROJECT_ID}_${FAMILY_ID}.yaml $CONFIG_DIR/
--
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