From 2c3689578b45833b293f0985e0e477ba29ba1ccc Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 6 Jan 2021 20:17:16 -0600
Subject: [PATCH] Add ambiguous species error reporting
---
workflow/rna-seq.nf | 68 +++++++++++++++++++++++++++++++++++++++++++--
1 file changed, 66 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 4cf0ef9..7d439ec 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -772,6 +772,7 @@ process inferMetadata {
output:
path "infer.csv" into inferMetadata_fl
path "${repRID}.infer_experiment.txt" into inferExperiment
+ path "speciesError.csv" into speciesError_fl
when:
fastqCountError_inferMetadata == "false"
@@ -802,6 +803,7 @@ process inferMetadata {
fi
echo -e "LOG: inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log
+ speciesError=false
# determine species
if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 40)) ]
then
@@ -817,7 +819,8 @@ process inferMetadata {
echo -e "LOG: ERROR - inference of species returns an ambiguous result: hu=\${align_hu} mo=\${align_mo}" >> ${repRID}.inferMetadata.log
if [ "${speciesForce}" == "" ]
then
- exit 1
+ speciesError=true
+ speciesError_details="**Inference of species returns an ambiguous result:** Percent aligned to human = \${align_hu}, percent aligned to mouse = \${align_mo}"
fi
fi
if [ "${speciesForce}" != "" ]
@@ -869,6 +872,9 @@ process inferMetadata {
# write inferred metadata to file
echo "\${ends},\${stranded},\${spike},\${species},\${align_ercc},\${align_hu},\${align_mo},\${percentF},\${percentR},\${fail}" 1>> infer.csv
+
+ # save species error file
+ echo -e "\${speciesError},\${speciesError}" > speciesError.csv
"""
}
@@ -930,6 +936,32 @@ speciesInfer.into {
speciesInfer_failExecutionRun
}
+// Split species count error into separate channel
+speciesCountError = Channel.create()
+speciesCountError_details = Channel.create()
+speciesError_fl.splitCsv(sep: ",", header: false).separate(
+ speciesCountError,
+ speciesCountError_details
+)
+
+// Replicate errors for multiple process inputs
+fastqCountError.into {
+ fastqCountError_checkMetadata
+ fastqCountError_uploadExecutionRun
+ fastqCountError_getRef
+ fastqCountError_alignData
+ fastqCountError_dedupData
+ fastqCountError_makeBigWig
+ fastqCountError_countData
+ fastqCountError_fastqc
+ fastqCountError_dataQC
+ fastqCountError_aggrQC
+ fastqCountError_uploadQC
+ fastqCountError_uploadProcessedFile
+ fastqCountError_uploadOutputBag
+ fastqCountError_failPreExecutionRun
+}
+
/*
* checkMetadata: checks the submitted metada against inferred
*/
@@ -947,6 +979,7 @@ process checkMetadata {
val speciesInfer from speciesInfer_checkMetadata
val fastqCountError_checkMetadata
val fastqReadError_checkMetadata
+ val speciesError_checkMetadata
output:
path ("check.csv") into checkMetadata_fl
@@ -955,6 +988,7 @@ process checkMetadata {
when:
fastqCountError_checkMetadata == "false"
fastqReadError_checkMetadata == "false"
+ speciesError_checkMetadata == "false"
script:
"""
@@ -1136,6 +1170,7 @@ process uploadExecutionRun {
val inputBagRID from inputBagRID_uploadExecutionRun
val fastqCountError_uploadExecutionRun
val fastqReadError_uploadExecutionRun
+ val speciesError_uploadExecutionRun
output:
path ("executionRunRID.csv") into executionRunRID_fl
@@ -1144,6 +1179,7 @@ process uploadExecutionRun {
upload
fastqCountError_uploadExecutionRun == "false"
fastqReadError_uploadExecutionRun == "false"
+ speciesReadError_uploadExecutionRun == "false"
script:
"""
@@ -1222,6 +1258,7 @@ process getRef {
val species from speciesInfer_getRef
val fastqCountError_getRef
val fastqReadError_getRef
+ val speciesError_getRef
val pipelineError_getRef
output:
@@ -1230,6 +1267,7 @@ process getRef {
when:
fastqCountError_getRef == "false"
fastqReadError_getRef == "false"
+ speciesError_getRef == "false"
pipelineError_getRef == "false"
script:
@@ -1320,6 +1358,7 @@ process alignData {
val stranded from strandedInfer_alignData
val fastqCountError_alignData
val fastqReadError_alignData
+ val speciesError_alignData
val pipelineError_alignData
output:
@@ -1329,6 +1368,7 @@ process alignData {
when:
fastqCountError_alignData == "false"
fastqReadError_alignData == "false"
+ speciesError_alignData == "false"
pipelineError_alignData == "false"
script:
@@ -1395,6 +1435,7 @@ process dedupData {
tuple path (bam), path (bai) from rawBam_dedupData
val fastqCountError_dedupData
val fastqReadError_dedupData
+ val speciesError_dedupData
val pipelineError_dedupData
output:
@@ -1405,6 +1446,7 @@ process dedupData {
when:
fastqCountError_dedupData == 'false'
fastqReadError_dedupData == 'false'
+ speciesError_dedupData == 'false'
pipelineError_dedupData == 'false'
script:
@@ -1452,6 +1494,7 @@ process makeBigWig {
tuple path (bam), path (bai) from dedupBam_makeBigWig
val fastqCountError_makeBigWig
val fastqReadError_makeBigWig
+ val speciesError_makeBigWig
val pipelineError_makeBigWig
output:
@@ -1460,6 +1503,7 @@ process makeBigWig {
when:
fastqCountError_makeBigWig == 'false'
fastqReadError_makeBigWig == 'false'
+ speciesError_makeBigWig == 'false'
pipelineError_makeBigWig == 'false'
script:
@@ -1490,6 +1534,7 @@ process countData {
val stranded from strandedInfer_countData
val fastqCountError_countData
val fastqReadError_countData
+ val speciesError_countData
val pipelineError_countData
output:
@@ -1500,6 +1545,7 @@ process countData {
when:
fastqCountError_countData == 'false'
fastqReadError_countData == 'false'
+ speciesError_countData == 'false'
pipelineError_countData == 'false'
script:
@@ -1569,6 +1615,7 @@ process fastqc {
path (fastq) from fastqs_fastqc
val fastqCountError_fastqc
val fastqReadError_fastqc
+ val speciesError_fastqc
val pipelineError_fastqc
output:
@@ -1578,6 +1625,7 @@ process fastqc {
when:
fastqCountError_fastqc == 'false'
fastqReadError_fastqc == 'false'
+ speciesError_fastqc == 'false'
pipelineError_fastqc == 'false'
script:
@@ -1620,6 +1668,7 @@ process dataQC {
val ends from endsInfer_dataQC
val fastqCountError_dataQC
val fastqReadError_dataQC
+ val speciesError_dataQC
val pipelineError_dataQC
output:
@@ -1630,6 +1679,7 @@ process dataQC {
when:
fastqCountError_dataQC == 'false'
fastqReadError_dataQC == 'false'
+ speciesError_dataQC == 'false'
pipelineError_dataQC == 'false'
script:
@@ -1708,6 +1758,7 @@ process aggrQC {
val expRID from expRID_aggrQC
val fastqCountError_aggrQC
val fastqReadError_aggrQC
+ val speciesError_aggrQC
val pipelineError_aggrQC
output:
@@ -1717,6 +1768,7 @@ process aggrQC {
when:
fastqCountError_aggrQC == 'false'
fastqReadError_aggrQC == 'false'
+ speciesError_aggrQC == 'false'
pipelineError_aggrQC == 'false'
script:
@@ -1803,6 +1855,7 @@ process uploadQC {
val finalCount from assignedReadsInfer_uploadQC
val fastqCountError_uploadQC
val fastqReadError_uploadQC
+ val speciesError_uploadQC
val pipelineError_uploadQC
output:
@@ -1812,6 +1865,7 @@ process uploadQC {
upload
fastqCountError_uploadQC == 'false'
fastqReadError_uploadQC == 'false'
+ speciesError_uploadQC == 'false'
pipelineError_uploadQC == 'false'
script:
@@ -1877,6 +1931,7 @@ process uploadProcessedFile {
val executionRunRID from executionRunRID_uploadProcessedFile
val fastqCountError_uploadProcessedFile
val fastqReadError_uploadProcessedFile
+ val speciesError_uploadProcessedFile
val pipelineError_uploadProcessedFile
output:
@@ -1886,6 +1941,7 @@ process uploadProcessedFile {
upload
fastqCountError_uploadProcessedFile == 'false'
fastqReadError_uploadProcessedFile == 'false'
+ speciesError_uploadProcessedFile == 'false'
pipelineError_uploadProcessedFile == 'false'
script:
@@ -1967,6 +2023,7 @@ process uploadOutputBag {
val executionRunRID from executionRunRID_uploadOutputBag
val fastqCountError_uploadOutputBag
val fastqReadError_uploadOutputBag
+ val speciesError_uploadOutputBag
val pipelineError_uploadOutputBag
output:
@@ -1976,6 +2033,7 @@ process uploadOutputBag {
upload
fastqCountError_uploadOutputBag == 'false'
fastqReadError_uploadOutputBag == 'false'
+ speciesError_uploadOutputBag == 'false'
pipelineError_uploadOutputBag == 'false'
script:
@@ -2069,9 +2127,12 @@ process failPreExecutionRun {
val fastqCountError_details
val fastqReadError from fastqReadError_failPreExecutionRun
val fastqReadError_details
+ val speciesError from speciesError_failPreExecutionRun
+ val speciesError_details
+
when:
upload
- fastqCountError == 'true' || fastqReadError == 'true'
+ fastqCountError == 'true' || fastqReadError == 'true' || speciesError == 'true'
script:
"""
@@ -2085,6 +2146,9 @@ process failPreExecutionRun {
elif [ ${fastqReadError} == true ]
then
errorDetails=\$(echo \$(errorDetails)${fastqReadError_details}"\\n")
+ elif [ ${speciesError} == true ]
+ then
+ errorDetails=\$(echo \$(errorDetails)${speciesError_details}"\\n")
fi
echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun.log
--
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