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Commit 356edbb6 authored by user name's avatar user name
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Mapping to family ids improved

parent 2d5c6dda
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1 merge request!3Ultra 2 SOP/doc updates
#!/bin/bash #!/bin/bash
#SBATCH --cpus-per-task=32 #SBATCH --cpus-per-task=16
#SBATCH --mem=8GB #SBATCH --mem=8GB
#SBATCH --time=48:00:00 #SBATCH --time=48:00:00
#SBATCH --job-name=trio_whole_exome_bcbio #SBATCH --job-name=trio_whole_exome_bcbio
...@@ -17,7 +17,8 @@ FAMILY_ID=`head -n $SLURM_ARRAY_TASK_ID $PARAMS_DIR/$PROJECT_ID.family_ids.txt | ...@@ -17,7 +17,8 @@ FAMILY_ID=`head -n $SLURM_ARRAY_TASK_ID $PARAMS_DIR/$PROJECT_ID.family_ids.txt |
SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'` SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
CONFIG_FILE=$CONFIG_DIR/${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}.yaml CONFIG_FILE=$CONFIG_DIR/*_${FAMILY_ID}.yaml
mkdir -p $WORK_DIR/$FAMILY_ID mkdir -p $WORK_DIR/$FAMILY_ID
cd $WORK_DIR/$FAMILY_ID cd $WORK_DIR/$FAMILY_ID
......
...@@ -19,7 +19,7 @@ SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'` ...@@ -19,7 +19,7 @@ SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
# This assumes that ${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID} is unique, and it should be - # This assumes that ${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID} is unique, and it should be -
# if there was a re-run of a family, it should have a new project id and version. # if there was a re-run of a family, it should have a new project id and version.
cd $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/families/*${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID} cd $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/families/*_${FAMILY_ID}
for BAM in */*.bam for BAM in */*.bam
do do
......
...@@ -19,7 +19,7 @@ SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'` ...@@ -19,7 +19,7 @@ SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
# This assumes that ${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID} is unique, and it should be - # This assumes that ${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID} is unique, and it should be -
# if there was a re-run of a family, it should have a new project id and version. # if there was a re-run of a family, it should have a new project id and version.
cd $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/families/*${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID} cd $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/families/*_${FAMILY_ID}
rm md5sum.txt 2> /dev/null rm md5sum.txt 2> /dev/null
......
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