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Commit 3c5f30fb authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Utilize seq type inference from seqwho

parent 34803354
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2 merge requests!76Develop,!71Seqwho
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CHANGELOG.md
+ 1
− 0
View file @ 3c5f30fb
......@@ -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)
......
workflow/rna-seq.nf
+ 129
− 60
View file @ 3c5f30fb
......@@ -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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