# HG changeset patch
# User bcclaywell
# Date 1427403369 14400
# Node ID 2d023c621bd0e6a95ba33432246df686c50aa771
# Parent 5f0648f799a91a2d34cba74cbcb535763839592d
Uploaded
diff -r 5f0648f799a9 -r 2d023c621bd0 filter-wrapper.sh
--- a/filter-wrapper.sh Wed Mar 25 19:25:27 2015 -0400
+++ b/filter-wrapper.sh Thu Mar 26 16:56:09 2015 -0400
@@ -30,3 +30,15 @@
fi
mv filtered.fasta ${FILTERED_SEQS}
+
+sequencing_quality_report.py ${PLATE_JSON} -t "Sequencing quality report" -o ${SQR_DIR}
+
+cat < ${SQR}
+
+
+
+
+ Sequencing quality report
+
+
+EOF
diff -r 5f0648f799a9 -r 2d023c621bd0 filter.xml
--- a/filter.xml Wed Mar 25 19:25:27 2015 -0400
+++ b/filter.xml Thu Mar 26 16:56:09 2015 -0400
@@ -1,4 +1,4 @@
-
+
sequences
yapp_env
@@ -31,8 +31,21 @@
+
+
+{
+ "plate": ${plate_id},
+ "name": "Plate ${plate_id}",
+ "zones": [
+ {
+ "zone": ${zone_id},
+ "cleaning_stats": "${filter_details}"
+ }
+ ]
+}
+
RAW_SEQS="${raw_seqs}"
INPUT_QUAL="${input_qual}"
@@ -41,11 +54,14 @@
MIN_LENGTH="${min_length}"
MIN_QUALITY="${min_quality}"
REVERSE_COMPLEMENT="${reverse_complement}"
+PLATE_JSON="${plate_json}"
FILTERED_SEQS="${filtered_seqs}"
FILTER_REPORT="${filter_report}"
FILTER_DETAILS="${filter_details}"
SPLIT_MAP="${split_map}"
+SQR="${seq_qual_report}"
+SQR_DIR="${seq_qual_report.files_path}"