From ac1c64c496559a529c2164429f4b2818b502977c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 9 Jan 2021 14:06:49 -0600
Subject: [PATCH] Add median TIN to mRNA_QC table
---
.gitlab-ci.yml | 2 +-
CHANGELOG.md | 1 +
workflow/rna-seq.nf | 11 +++++++++--
workflow/scripts/upload_qc.py | 3 +++
4 files changed, 14 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 03f5ebe..bf7355a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -389,7 +389,7 @@ uploadQC:
done
echo all old mRNA QC RIDs deleted
fi
- rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BVDJ -p "Single Read" -s forward -l 35 -w 5 -f 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
+ rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BVDJ -p "Single Read" -s forward -l 35 -w 5 -f 1 -t 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
echo ${rid} test mRNA QC created
uploadProcessedFile:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f1e3982..206089b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,7 @@
# v1.0.0 (in development)
**User Facing**
* Add link to reference builder script
+* Output median TIN to mRNA_QC table
**Background**
* Change consistency test to check if +/- 1% of standard
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 8c247c2..21a2ace 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1734,6 +1734,12 @@ tinMedInfer_fl.splitCsv(sep: ",", header: false).separate(
tinMedInfer
)
+// Replicate inferred median TIN for multiple process inputs
+tinMedInfer.into {
+ tinMedInfer_aggrQC
+ tinMedInfer_uploadQC
+}
+
/*
*aggrQC: aggregate QC from processes as well as metadata and run MultiQC
*/
@@ -1769,7 +1775,7 @@ process aggrQC {
val readLengthI from readLengthInfer_aggrQC
val rawReadsI from rawReadsInfer_aggrQC
val assignedReadsI from assignedReadsInfer_aggrQC
- val tinMedI from tinMedInfer
+ val tinMedI from tinMedInfer_aggrQC
val studyRID from studyRID_aggrQC
val expRID from expRID_aggrQC
val fastqCountError_aggrQC
@@ -1869,6 +1875,7 @@ process uploadQC {
val length from readLengthInfer_uploadQC
val rawCount from rawReadsInfer_uploadQC
val finalCount from assignedReadsInfer_uploadQC
+ val tinMed from tinMedInfer_uploadQC
val fastqCountError_uploadQC
val fastqReadError_uploadQC
val speciesError_uploadQC
@@ -1912,7 +1919,7 @@ process uploadQC {
echo LOG: all old mRNA QC RIDs deleted >> ${repRID}.uploadQC.log
fi
- qc_rid=\$(python3 ${script_uploadQC} -r ${repRID} -e ${executionRunRID} -p "\${end}" -s ${stranded} -l ${length} -w ${rawCount} -f ${finalCount} -o ${source} -c \${cookie} -u F)
+ qc_rid=\$(python3 ${script_uploadQC} -r ${repRID} -e ${executionRunRID} -p "\${end}" -s ${stranded} -l ${length} -w ${rawCount} -f ${finalCount} -t ${tinMed} -o ${source} -c \${cookie} -u F)
echo LOG: mRNA QC RID uploaded - \${qc_rid} >> ${repRID}.uploadQC.log
echo "\${qc_rid}" > qcRID.csv
diff --git a/workflow/scripts/upload_qc.py b/workflow/scripts/upload_qc.py
index 930896d..b842a7a 100644
--- a/workflow/scripts/upload_qc.py
+++ b/workflow/scripts/upload_qc.py
@@ -12,6 +12,7 @@ def get_args():
parser.add_argument('-l', '--length', help="median read length", required=True)
parser.add_argument('-w', '--rawCount', help="raw count", required=True)
parser.add_argument('-f', '--assignedCount', help="final assigned count", required=True)
+ parser.add_argument('-t', '--tin', help="median TIN", required=True)
parser.add_argument('-n', '--notes', help="notes", default="", required=False)
parser.add_argument('-o', '--host', help="datahub host", required=True)
parser.add_argument('-c', '--cookie', help="cookie token", required=True)
@@ -33,6 +34,7 @@ def main(hostname, catalog_number, credential):
"Median_Read_Length": args.length,
"Raw_Count": args.rawCount,
"Final_Count": args.assignedCount,
+ "Median_TIN": args.tin,
"Notes": args.notes
}
entities = run_table.insert([run_data])
@@ -47,6 +49,7 @@ def main(hostname, catalog_number, credential):
"Median_Read_Length": args.length,
"Raw_Count": args.rawCount,
"Final_Count": args.assignedCount,
+ "Median_TIN": args.tin,
"Notes": args.notes
}
entities = run_table.update([run_data])
--
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