From 3c5f30fb8c550a18428bb4e6754b0bde4c2fd984 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 19 Feb 2021 14:00:19 -0600
Subject: [PATCH] Utilize seq type inference from seqwho
---
CHANGELOG.md | 1 +
workflow/rna-seq.nf | 189 ++++++++++++++++++++++++++++++--------------
2 files changed, 130 insertions(+), 60 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 947a384..faa11d1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,7 @@
* Strandedness metadata "yes"/"no" changed to boolean "t"/"f" in data-hub, pipeline updated to handle (#70) ("yes"/"no" still acceptable for backwards compatibility)
* Upload empty mRNA_QC entry if data error (#111)
* Allow forcing of strandedness and spike (#100)
+* Add seqwho
**Background**
* Add memory limit (75%) per thread for samtools sort (#108)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 631963f..7545b25 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -700,7 +700,7 @@ process seqwho {
val fastqFileError_seqwho
output:
- path
+ path "inferError.csv" into inferError_fl
when:
fastqCountError_seqwho == "false"
@@ -717,7 +717,7 @@ process seqwho {
echo -e "LOG: seqwho index downloaded" >> ${repRID}.seqwho.log
# run seqwho
- python3 seqwho.py -f *.fastq.gz -x SeqWho.ix
+ seqwho.py -f *.fastq.gz -x SeqWho.ix
echo -e "LOG: seqwho ran" >> ${repRID}.seqwho.log
# parse inference from R1
@@ -778,7 +778,7 @@ process seqwho {
fi
if [ \${seqtypeConfidenceR2} == "1" ]
then
- seqtypeConfidenceR1="high"
+ seqtypeConfidenceR2="high"
else
seqtypeConfidenceR2="low"
fi
@@ -787,8 +787,8 @@ process seqwho {
# detect errors
speciesInferError=false
speciesInferError_details=""
- seqtpeInferError=false
- seqtpeInferError_details=""
+ seqtypeInferError=false
+ seqtypeInferError_details=""
if [ "\${confidenceR1}" == "high" ] && [ "\${confidenceR2}" == "high" ]
then
echo -e "LOG: high confidence inference detected" >> ${repRID}.seqwho.log
@@ -808,14 +808,14 @@ process seqwho {
seqtpeInfer="rnaseq"
echo -e "LOG: concordant rnaseq seq type inference detected" >> ${repRID}.seqwho.log
else
- seqtpeInferError=true
- seqtpeInferError_details="**Infered sequencing type is not mRNA-seq:** Infered = \${seqtypeR1}"
- echo -e "LOG: inference error: \${seqtpeInferError_details}" >> ${repRID}.seqwho.log
+ seqtypeInferError=true
+ seqtypeInferError_details="**Infered sequencing type is not mRNA-seq:** Infered = \${seqtypeR1}"
+ echo -e "LOG: inference error: \${seqtypeInferError_details}" >> ${repRID}.seqwho.log
fi
else
- seqtpeInferError=true
- seqtpeInferError_details="**Infered sequencing type does not match for R1 and R2:** Infered R1 = \${seqtypeR1} and infered R2 = \${seqtypeR2}"
- echo -e "LOG: inference error: \${seqtpeInferError_details}" >> ${repRID}.seqwho.log
+ seqtypeInferError=true
+ seqtypeInferError_details="**Infered sequencing type does not match for R1 and R2:** Infered R1 = \${seqtypeR1} and infered R2 = \${seqtypeR2}"
+ echo -e "LOG: inference error: \${seqtypeInferError_details}" >> ${repRID}.seqwho.log
fi
else
speciesInferError=true
@@ -829,9 +829,42 @@ process seqwho {
fi
echo -e "LOG: inference error: \${speciesInferError_details}" >> ${repRID}.seqwho.log
fi
+
+ # save error file
+ echo "\${seqtypeInferError},\${seqtypeInferError_details}" > inferError.csv
"""
}
+// Split species error into separate channel
+seqtypeInferError = Channel.create()
+seqtypeInferError_details = Channel.create()
+inferError_fl.splitCsv(sep: ",", header: false).separate(
+ seqtypeInferError,
+ seqtypeInferError_details
+)
+
+// Replicate errors for multiple process inputs
+seqtypeInferError.into {
+ seqtypeInferError_trimData
+ seqtypeInferError_getRefInfer
+ seqtypeInferError_downsampleData
+ seqtypeInferError_alignSampleData
+ seqtypeInferError_inferMetadata
+ seqtypeInferError_checkMetadata
+ seqtypeInferError_uploadExecutionRun
+ seqtypeInferError_getRef
+ seqtypeInferError_alignData
+ seqtypeInferError_dedupData
+ seqtypeInferError_makeBigWig
+ seqtypeInferError_countData
+ seqtypeInferError_dataQC
+ seqtypeInferError_aggrQC
+ seqtypeInferError_uploadQC
+ seqtypeInferError_uploadQC_fail
+ seqtypeInferError_uploadProcessedFile
+ seqtypeInferError_uploadOutputBag
+}
+
/*
* trimData: trims any adapter or non-host sequences from the data
*/
@@ -844,6 +877,7 @@ process trimData {
val fastqCountError_trimData
val fastqReadError_trimData
val fastqFileError_trimData
+ val seqtypeInferError_trimData
output:
path ("*.fq.gz") into fastqsTrim
@@ -854,6 +888,7 @@ process trimData {
fastqCountError_trimData == "false"
fastqReadError_trimData == "false"
fastqFileError_trimData == "false"
+ seqtypeInferError_trimData == "false"
script:
"""
@@ -897,7 +932,7 @@ fastqsTrim.into {
}
// Combine inputs of getRefInfer
-getRefInferInput = referenceInfer.combine(deriva_getRefInfer.combine(script_refDataInfer.combine(fastqCountError_getRefInfer.combine(fastqReadError_getRefInfer.combine(fastqFileError_getRefInfer)))))
+getRefInferInput = referenceInfer.combine(deriva_getRefInfer.combine(script_refDataInfer.combine(fastqCountError_getRefInfer.combine(fastqReadError_getRefInfer.combine(fastqFileError_getRefInfer.combine(seqtypeInferError_getRefInfer))))))
/*
* getRefInfer: dowloads appropriate reference for metadata inference
@@ -906,7 +941,7 @@ process getRefInfer {
tag "${refName}"
input:
- tuple val (refName), path (credential, stageAs: "credential.json"), path (script_refDataInfer), val (fastqCountError), val (fastqReadError), val (fastqFileError) from getRefInferInput
+ tuple val (refName), path (credential, stageAs: "credential.json"), path (script_refDataInfer), val (fastqCountError), val (fastqReadError), val (fastqFileError), val (seqtypeInferError) from getRefInferInput
output:
tuple val (refName), path ("hisat2", type: 'dir'), path ("*.fna"), path ("*.gtf") into refInfer
@@ -916,6 +951,7 @@ process getRefInfer {
fastqCountError == "false"
fastqReadError == "false"
fastqFileError == "false"
+ seqtypeInferError == "false"
script:
"""
@@ -994,6 +1030,7 @@ process downsampleData {
val fastqCountError_downsampleData
val fastqReadError_downsampleData
val fastqFileError_downsampleData
+ val seqtypeInferError_downsampleData
output:
path ("sampled.1.fq") into fastqs1Sample
@@ -1003,6 +1040,7 @@ process downsampleData {
fastqCountError_downsampleData == "false"
fastqReadError_downsampleData == "false"
fastqFileError_downsampleData == "false"
+ seqtypeInferError_downsampleData == "false"
script:
"""
@@ -1026,7 +1064,7 @@ process downsampleData {
}
// Replicate the dowsampled fastq's and attatched to the references
-inferInput = endsManual_alignSampleData.combine(refInfer.combine(fastqs1Sample.collect().combine(fastqs2Sample.collect().combine(fastqCountError_alignSampleData.combine(fastqReadError_alignSampleData.combine(fastqFileError_alignSampleData))))))
+inferInput = endsManual_alignSampleData.combine(refInfer.combine(fastqs1Sample.collect().combine(fastqs2Sample.collect().combine(fastqCountError_alignSampleData.combine(fastqReadError_alignSampleData.combine(fastqFileError_alignSampleData.combine(seqtypeInferError_alignSampleData)))))))
/*
* alignSampleData: aligns the downsampled reads to a reference database
@@ -1035,7 +1073,7 @@ process alignSampleData {
tag "${ref}"
input:
- tuple val (ends), val (ref), path (hisat2), path (fna), path (gtf), path (fastq1), path (fastq2), val (fastqCountError), val (fastqReadError), val (fastqFileError) from inferInput
+ tuple val (ends), val (ref), path (hisat2), path (fna), path (gtf), path (fastq1), path (fastq2), val (fastqCountError), val (fastqReadError), val (fastqFileError), val (seqtypeInferError) from inferInput
output:
path ("${ref}.sampled.sorted.bam") into sampleBam
@@ -1046,6 +1084,7 @@ process alignSampleData {
fastqCountError == "false"
fastqReadError == "false"
fastqFileError == "false"
+ seqtypeInferError == "false"
script:
"""
@@ -1100,6 +1139,7 @@ process inferMetadata {
val fastqCountError_inferMetadata
val fastqReadError_inferMetadata
val fastqFileError_inferMetadata
+ val seqtypeInferError_inferMetadata
output:
path "infer.csv" into inferMetadata_fl
@@ -1110,6 +1150,7 @@ process inferMetadata {
fastqCountError_inferMetadata == "false"
fastqReadError_inferMetadata == "false"
fastqFileError_inferMetadata == "false"
+ seqtypeInferError_inferMetadata == "false"
script:
"""
@@ -1338,7 +1379,9 @@ process checkMetadata {
val speciesInfer from speciesInfer_checkMetadata
val fastqCountError_checkMetadata
val fastqReadError_checkMetadata
+ val seqtypeInferError_checkMetadata
val fastqFileError_checkMetadata
+
val speciesError_checkMetadata
output:
@@ -1349,6 +1392,7 @@ process checkMetadata {
fastqCountError_checkMetadata == "false"
fastqReadError_checkMetadata == "false"
fastqFileError_checkMetadata == "false"
+ seqtypeInferError_checkMetadata == "false"
speciesError_checkMetadata == "false"
script:
@@ -1556,6 +1600,7 @@ process uploadExecutionRun {
val fastqCountError_uploadExecutionRun
val fastqReadError_uploadExecutionRun
val fastqFileError_uploadExecutionRun
+ val seqtypeInferError_uploadExecutionRun
val speciesError_uploadExecutionRun
output:
@@ -1566,6 +1611,7 @@ process uploadExecutionRun {
fastqCountError_uploadExecutionRun == "false"
fastqReadError_uploadExecutionRun == "false"
fastqFileError_uploadExecutionRun == "false"
+ seqtypeInferError_uploadExecutionRun == "false"
speciesError_uploadExecutionRun == "false"
script:
@@ -1657,6 +1703,7 @@ process getRef {
val fastqCountError_getRef
val fastqReadError_getRef
val fastqFileError_getRef
+ val seqtypeInferError_getRef
val speciesError_getRef
val pipelineError_getRef
@@ -1667,6 +1714,7 @@ process getRef {
fastqCountError_getRef == "false"
fastqReadError_getRef == "false"
fastqFileError_getRef == "false"
+ seqtypeInferError_getRef == "false"
speciesError_getRef == "false"
pipelineError_getRef == "false"
@@ -1759,6 +1807,7 @@ process alignData {
val fastqCountError_alignData
val fastqReadError_alignData
val fastqFileError_alignData
+ val seqtypeInferError_alignData
val speciesError_alignData
val pipelineError_alignData
@@ -1770,6 +1819,7 @@ process alignData {
fastqCountError_alignData == "false"
fastqReadError_alignData == "false"
fastqFileError_alignData == "false"
+ seqtypeInferError_alignData == "false"
speciesError_alignData == "false"
pipelineError_alignData == "false"
@@ -1841,6 +1891,7 @@ process dedupData {
val fastqCountError_dedupData
val fastqReadError_dedupData
val fastqFileError_dedupData
+ val seqtypeInferError_dedupData
val speciesError_dedupData
val pipelineError_dedupData
@@ -1850,11 +1901,12 @@ process dedupData {
path ("*.deduped.Metrics.txt") into dedupQC
when:
- fastqCountError_dedupData == 'false'
- fastqReadError_dedupData == 'false'
- fastqFileError_dedupData == 'false'
- speciesError_dedupData == 'false'
- pipelineError_dedupData == 'false'
+ fastqCountError_dedupData == "false"
+ fastqReadError_dedupData == "false"
+ fastqFileError_dedupData == "false"
+ seqtypeInferError_dedupData == "false"
+ speciesError_dedupData == "false"
+ pipelineError_dedupData == "false"
script:
"""
@@ -1902,6 +1954,7 @@ process makeBigWig {
val fastqCountError_makeBigWig
val fastqReadError_makeBigWig
val fastqFileError_makeBigWig
+ val seqtypeInferError_makeBigWig
val speciesError_makeBigWig
val pipelineError_makeBigWig
@@ -1909,11 +1962,12 @@ process makeBigWig {
path ("${repRID}_sorted.deduped.bw") into bigwig
when:
- fastqCountError_makeBigWig == 'false'
- fastqReadError_makeBigWig == 'false'
- fastqFileError_makeBigWig == 'false'
- speciesError_makeBigWig == 'false'
- pipelineError_makeBigWig == 'false'
+ fastqCountError_makeBigWig == "false"
+ fastqReadError_makeBigWig == "false"
+ fastqFileError_makeBigWig == "false"
+ seqtypeInferError_makeBigWig == "false"
+ speciesError_makeBigWig == "false"
+ pipelineError_makeBigWig == "false"
script:
"""
@@ -1944,6 +1998,7 @@ process countData {
val fastqCountError_countData
val fastqReadError_countData
val fastqFileError_countData
+ val seqtypeInferError_countData
val speciesError_countData
val pipelineError_countData
@@ -1953,11 +2008,12 @@ process countData {
path ("assignedReads.csv") into assignedReadsInfer_fl
when:
- fastqCountError_countData == 'false'
- fastqReadError_countData == 'false'
- fastqFileError_countData == 'false'
- speciesError_countData == 'false'
- pipelineError_countData == 'false'
+ fastqCountError_countData == "false"
+ fastqReadError_countData == "false"
+ fastqFileError_countData == "false"
+ seqtypeInferError_countData == "false"
+ speciesError_countData == "false"
+ pipelineError_countData == "false"
script:
"""
@@ -2031,6 +2087,7 @@ process dataQC {
val fastqCountError_dataQC
val fastqReadError_dataQC
val fastqFileError_dataQC
+ val seqtypeInferError_dataQC
val speciesError_dataQC
val pipelineError_dataQC
@@ -2040,11 +2097,12 @@ process dataQC {
path "${repRID}_insertSize.inner_distance_freq.txt" into innerDistance
when:
- fastqCountError_dataQC == 'false'
- fastqReadError_dataQC == 'false'
- fastqFileError_dataQC == 'false'
- speciesError_dataQC == 'false'
- pipelineError_dataQC == 'false'
+ fastqCountError_dataQC == "false"
+ fastqReadError_dataQC == "false"
+ fastqFileError_dataQC == "false"
+ seqtypeInferError_dataQC == "false"
+ speciesError_dataQC == "false"
+ pipelineError_dataQC == "false"
script:
"""
@@ -2129,6 +2187,7 @@ process aggrQC {
val fastqCountError_aggrQC
val fastqReadError_aggrQC
val fastqFileError_aggrQC
+ val seqtypeInferError_aggrQC
val speciesError_aggrQC
val pipelineError_aggrQC
@@ -2137,11 +2196,12 @@ process aggrQC {
path "${repRID}.multiqc_data.json" into multiqcJSON
when:
- fastqCountError_aggrQC == 'false'
- fastqReadError_aggrQC == 'false'
- fastqFileError_aggrQC == 'false'
- speciesError_aggrQC == 'false'
- pipelineError_aggrQC == 'false'
+ fastqCountError_aggrQC == "false"
+ fastqReadError_aggrQC == "false"
+ fastqFileError_aggrQC == "false"
+ seqtypeInferError_aggrQC == "false"
+ speciesError_aggrQC == "false"
+ pipelineError_aggrQC == "false"
script:
"""
@@ -2258,6 +2318,7 @@ process uploadQC {
val fastqCountError_uploadQC
val fastqReadError_uploadQC
val fastqFileError_uploadQC
+ val seqtypeInferError_uploadQC
val speciesError_uploadQC
val pipelineError_uploadQC
@@ -2266,11 +2327,12 @@ process uploadQC {
when:
upload
- fastqCountError_uploadQC == 'false'
- fastqReadError_uploadQC == 'false'
- fastqFileError_uploadQC == 'false'
- speciesError_uploadQC == 'false'
- pipelineError_uploadQC == 'false'
+ fastqCountError_uploadQC == "false"
+ fastqReadError_uploadQC == "false"
+ fastqFileError_uploadQC == "false"
+ seqtypeInferError_uploadQC == "false"
+ speciesError_uploadQC == "false"
+ pipelineError_uploadQC == "false"
script:
"""
@@ -2330,6 +2392,7 @@ process uploadProcessedFile {
val fastqCountError_uploadProcessedFile
val fastqReadError_uploadProcessedFile
val fastqFileError_uploadProcessedFile
+ val seqtypeInferError_uploadProcessedFile
val speciesError_uploadProcessedFile
val pipelineError_uploadProcessedFile
@@ -2338,11 +2401,12 @@ process uploadProcessedFile {
when:
upload
- fastqCountError_uploadProcessedFile == 'false'
- fastqReadError_uploadProcessedFile == 'false'
- fastqFileError_uploadProcessedFile == 'false'
- speciesError_uploadProcessedFile == 'false'
- pipelineError_uploadProcessedFile == 'false'
+ fastqCountError_uploadProcessedFile == "false"
+ fastqReadError_uploadProcessedFile == "false"
+ fastqFileError_uploadProcessedFile == "false"
+ seqtypeInferError_uploadProcessedFile == "false"
+ speciesError_uploadProcessedFile == "false"
+ pipelineError_uploadProcessedFile == "false"
script:
"""
@@ -2424,6 +2488,7 @@ process uploadOutputBag {
val fastqCountError_uploadOutputBag
val fastqReadError_uploadOutputBag
val fastqFileError_uploadOutputBag
+ val seqtypeInferError_uploadOutputBag
val speciesError_uploadOutputBag
val pipelineError_uploadOutputBag
@@ -2432,11 +2497,12 @@ process uploadOutputBag {
when:
upload
- fastqCountError_uploadOutputBag == 'false'
- fastqReadError_uploadOutputBag == 'false'
- fastqFileError_uploadOutputBag == 'false'
- speciesError_uploadOutputBag == 'false'
- pipelineError_uploadOutputBag == 'false'
+ fastqCountError_uploadOutputBag == "false"
+ fastqReadError_uploadOutputBag == "false"
+ fastqFileError_uploadOutputBag == "false"
+ seqtypeInferError_uploadOutputBag == "false"
+ speciesError_uploadOutputBag == "false"
+ pipelineError_uploadOutputBag == "false"
script:
"""
@@ -2532,12 +2598,12 @@ process finalizeExecutionRun {
}
// Combine errors
-error_meta = fastqCountError_uploadQC_fail.ifEmpty(false).combine(fastqReadError_uploadQC_fail.ifEmpty(false).combine(fastqFileError_uploadQC_fail.ifEmpty(false).combine(speciesError_uploadQC_fail.ifEmpty(false).combine(pipelineError_uploadQC_fail.ifEmpty(false)))))
+error_meta = fastqCountError_uploadQC_fail.ifEmpty(false).combine(fastqReadError_uploadQC_fail.ifEmpty(false).combine(fastqFileError_uploadQC_fail.ifEmpty(false).combine(seqtypeInferError_uploadQC_fail.ifEmpty(false).combine(speciesError_uploadQC_fail.ifEmpty(false).combine(pipelineError_uploadQC_fail.ifEmpty(false))))))
error_meta. into{
error_failPreExecutionRun
error_uploadQC_fail
}
-errorDetails = fastqCountError_details.ifEmpty("").combine(fastqReadError_details.ifEmpty("").combine(fastqFileError_details.ifEmpty("").combine(speciesError_details.ifEmpty(""))))
+errorDetails = fastqCountError_details.ifEmpty("").combine(fastqReadError_details.ifEmpty("").combine(fastqFileError_details.ifEmpty("").combine(seqtypeInferError_details.ifEmpty("").combine(speciesError_details.ifEmpty("")))))
/*
* failPreExecutionRun_fastq: fail the execution run prematurely for fastq errors
@@ -2551,15 +2617,15 @@ process failPreExecutionRun {
val spike from spikeMeta_failPreExecutionRun
val species from speciesMeta_failPreExecutionRun
val inputBagRID from inputBagRID_failPreExecutionRun
- tuple val (fastqCountError), val (fastqReadError), val (fastqFileError), val (speciesError), val (pipelineError) from error_failPreExecutionRun
- tuple val (fastqCountError_details), val (fastqReadError_details), val (fastqFileError_details), val (speciesError_details) from errorDetails
+ tuple val (fastqCountError), val (fastqReadError), val (fastqFileError), val (seqtypeInferError), val (speciesError), val (pipelineError) from error_failPreExecutionRun
+ tuple val (fastqCountError_details), val (fastqReadError_details), val (fastqFileError_details), val (seqtypeInferError_details), val (speciesError_details) from errorDetails
output:
path ("executionRunRID.csv") into executionRunRID_preFail_fl
when:
upload
- fastqCountError == 'true' || fastqReadError == 'true' || fastqFileError == 'true' || speciesError == 'true'
+ fastqCountError == "true" || fastqReadError == "true" || fastqFileError == "true" || seqtypeInferError == "true" || speciesError == "true"
script:
"""
@@ -2576,6 +2642,9 @@ process failPreExecutionRun {
elif [ ${fastqFileError} == true ]
then
errorDetails=\$(echo \$(errorDetails)${fastqFileError_details}"\\n")
+ elif [ ${seqtypeInferError} == true ]
+ then
+ errorDetails=\$(echo \$(errorDetails)${seqtypeInferError_details}"\\n")
elif [ ${speciesError} == true ]
then
errorDetails=\$(echo \$(errorDetails)${speciesError_details}"\\n")
--
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