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Commit 7a096fd5 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add handeling for low confidence seq type

parent b858a9d7
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2 merge requests!76Develop,!71Seqwho
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rna-seq.nf
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......@@ -740,6 +740,7 @@ process seqwho {
speciesConfidenceR2="1"
seqtypeConfidenceR2="1"
fi
cp SeqWho_call.tsv SeqWho_call_full.tsv
speciesErrorSeqwho=false
speciesErrorSeqwho_details=""
......@@ -791,41 +792,103 @@ process seqwho {
echo -e "LOG: inference error: \${speciesErrorSeqwho_details}" >> ${repRID}.seqwho.log
fi
# set seq type
if [ "\${seqtypeR1}" == "\${seqtypeR2}" ]
# detect species confidence errors
if [ "\${speciesConfidenceR1}" == "high" ] && [ "\${speciesConfidenceR2}" == "high" ]
then
if [ "\${seqtypeR1}" == "rnaseq" ]
echo -e "LOG: high confidence species inference detected" >> ${repRID}.seqwho.log
else
speciesErrorSeqwho=true
speciesErrorSeqwho_details=\$(echo "**Infered species confidence is low:**\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|Infered species confidence|\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|:--|:--:|\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|Read 1|\${speciesConfidenceR1}|\\n")
if [ "${ends}" == "pe" ]
then
seqtpeInfer="rnaseq"
echo -e "LOG: concordant rnaseq seq type inference detected" >> ${repRID}.seqwho.log
else
seqtypeError=true
seqtypeError_details="**Infered sequencing type is not mRNA-seq:** Infered = \${seqtypeR1}"
echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|Read 2|\${speciesConfidenceR2}|\\n")
fi
else
seqtypeError=true
seqtypeError_details="**Infered sequencing type does not match for R1 and R2:** Infered R1 = \${seqtypeR1} and infered R2 = \${seqtypeR2}"
echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
echo -e "LOG: inference error: \${speciesErrorSeqwho_details}" >> ${repRID}.seqwho.log
fi
# detect confidence errors
if [ "\${confidenceR1}" == "high" ] && [ "\${confidenceR2}" == "high" ]
# detect seq type errors and set type
if [ "\${seqtypeConfidenceR1}" == "high" ] && [ "\${seqtypeConfidenceR2}" == "high" ]
then
echo -e "LOG: high confidence inference detected" >> ${repRID}.seqwho.log
echo -e "LOG: high confidence seq type inference detected" >> ${repRID}.seqwho.log
# set seq type
if [ "\${seqtypeR1}" == "\${seqtypeR2}" ]
then
if [ "\${seqtypeR1}" == "rnaseq" ]
then
seqtpeInfer="rnaseq"
echo -e "LOG: concordant rnaseq seq type inference detected" >> ${repRID}.seqwho.log
else
seqtypeError=true
seqtypeError_details="**Infered sequencing type is not mRNA-seq:** Infered = \${seqtypeR1}"
echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
fi
else
seqtypeError=true
seqtypeError_details="**Infered sequencing type does not match for R1 and R2:** Infered R1 = \${seqtypeR1} and infered R2 = \${seqtypeR2}"
echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
fi
else
speciesErrorSeqwho=true
speciesErrorSeqwho_details=\$(echo "**Infered species and or sequencing type confidence is low:**\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|Infered species confidence|Infered sequencing type confidence|\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|:--|:--:|:--:|\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|Read 1|\${speciesConfidenceR1}|\${seqtypeConfidenceR1}|\\n")
echo -e "LOG: low confidence seq type inference detected" >> ${repRID}.seqwho.log
seqtk sample -s100 ${fastq[0]} 1000000 1> sampled.1.seed100.fastq &
seqtk sample -s200 ${fastq[0]} 1000000 1> sampled.1.seed200.fastq &
seqtk sample -s300 ${fastq[0]} 1000000 1> sampled.1.seed300.fastq &
wait
gzip sampled.1.seed100.fastq &
gzip sampled.1.seed200.fastq &
gzip sampled.1.seed300.fastq &
wait
seqwho.py -f sampled.1.seed*.fastq.gz -x SeqWho.ix
seqtypeR1_1=\$(cat SeqWho_call.tsv | grep sampled.1.seed100.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
seqtypeR1_2=\$(cat SeqWho_call.tsv | grep sampled.1.seed200.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
seqtypeR1_3=\$(cat SeqWho_call.tsv | grep sampled.1.seed300.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
cp SeqWho_call.tsv SeqWho_call_sampledR1.tsv
if [ "\${seqtypeR1_1}" == "\${seqtypeR1}" ] && [ "\${seqtypeR1_2}" == "\${seqtypeR1}" ] && [ "\${seqtypeR1_3}" == "\${seqtypeR1}" ]
then
concensus=true
else
concensus=false
fi
if [ "${ends}" == "pe" ]
then
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|Read 2|\${speciesConfidenceR2}|\${seqtypeConfidenceR2}|\\n")
seqtk sample -s100 ${fastq[1]} 1000000 1> sampled.2.seed100.fastq &
seqtk sample -s200 ${fastq[1]} 1000000 1> sampled.2.seed200.fastq &
seqtk sample -s300 ${fastq[1]} 1000000 1> sampled.2.seed300.fastq &
wait
gzip sampled.2.seed100.fastq &
gzip sampled.2.seed200.fastq &
gzip sampled.2.seed300.fastq &
wait
seqwho.py -f sampled.2.seed*.fastq.gz -x SeqWho.ix
seqtypeR2_1=\$(cat SeqWho_call.tsv | grep sampled.2.seed100.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
seqtypeR2_2=\$(cat SeqWho_call.tsv | grep sampled.2.seed200.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
seqtypeR2_3=\$(cat SeqWho_call.tsv | grep sampled.2.seed300.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ")
cp SeqWho_call.tsv SeqWho_call_sampledR2.tsv
if [ "\${seqtypeR2_1}" == "\${seqtypeR1}" ] && [ "\${seqtypeR2_2}" == "\${seqtypeR1}" ] && [ "\${seqtypeR2_3}" == "\${seqtypeR1}" ]
then
concensus=\${concensus}
else
concensus=false
fi
fi
if [ \${concensus} == false ]
then
seqtypeError=true
seqtypeError_details=\$(echo "**Infered species confidence is low:**\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|fastq|Infered seq type|Infered seq type confidence|\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|:--|:--:|:--:|\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|Read 1|\${seqtypeR1}|\${seqtypeConfidenceR1}|\\n")
if [ "${ends}" == "pe" ]
then
seqtypeError_details=\$(echo \${seqtypeError_details}"|Read 2|\${seqtypeR2}|\${seqtypeConfidenceR2}|\\n")
fi
echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
fi
echo -e "LOG: inference error: \${speciesErrorSeqwho_details}" >> ${repRID}.seqwho.log
fi
# check for species match error
if [ "${speciesMeta}" != "\${speciesInfer}" ]
then
if [ "${params.speciesForce}" != "" ]
......@@ -878,6 +941,7 @@ inferError_fl.splitCsv(sep: ",", header: false).separate(
speciesError
)
seqtypeError.into {
seqtypeError_trimData
seqtypeError_getRef
seqtypeError_downsampleData
seqtypeError_alignSampleDataERCC
......@@ -897,6 +961,27 @@ seqtypeError.into {
seqtypeError_finalizeExecutionRun
seqtypeError_uploadQC_fail
}
speciesErrorSeqwho.into {
speciesErrorSeqwho_trimData
speciesErrorSeqwho_getRef
speciesErrorSeqwho_downsampleData
speciesErrorSeqwho_alignSampleDataERCC
speciesErrorSeqwho_alignSampleData
speciesErrorSeqwho_inferMetadata
speciesErrorSeqwho_checkMetadata
speciesErrorSeqwho_alignData
speciesErrorSeqwho_dedupData
speciesErrorSeqwho_makeBigWig
speciesErrorSeqwho_countData
speciesErrorSeqwho_dataQC
speciesErrorSeqwho_aggrQC
speciesErrorSeqwho_uploadExecutionRun
speciesErrorSeqwho_uploadQC
speciesErrorSeqwho_uploadProcessedFile
speciesErrorSeqwho_uploadOutputBag
speciesErrorSeqwho_finalizeExecutionRun
speciesErrorSeqwho_uploadQC_fail
}
speciesError.into {
speciesError_checkMetadata
speciesError_uploadExecutionRun
......@@ -989,6 +1074,8 @@ process trimData {
val fastqCountError from fastqCountError_trimData
val fastqReadError from fastqReadError_trimData
val fastqFileError from fastqFileError_trimData
val seqtypeError from seqtypeError_trimData
val speciesErrorSeqwho from speciesErrorSeqwho_trimData
output:
path ("*.fq.gz") into fastqsTrim
......@@ -999,6 +1086,8 @@ process trimData {
fastqCountError == "false"
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
script:
"""
......@@ -1052,6 +1141,7 @@ process downsampleData {
val fastqReadError from fastqReadError_downsampleData
val fastqFileError from fastqFileError_downsampleData
val seqtypeError from seqtypeError_downsampleData
val speciesErrorSeqwho from speciesErrorSeqwho_downsampleData
output:
path ("sampled.{1,2}.fq") into fastqsSample
......@@ -1061,6 +1151,7 @@ process downsampleData {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
script:
"""
......@@ -1104,6 +1195,7 @@ process alignSampleDataERCC {
val fastqReadError from fastqReadError_alignSampleDataERCC
val fastqFileError from fastqFileError_alignSampleDataERCC
val seqtypeError from seqtypeError_alignSampleDataERCC
val speciesErrorSeqwho from speciesErrorSeqwho_alignSampleDataERCC
output:
path "inferSpike.csv" into inferSpike_fl
......@@ -1201,6 +1293,7 @@ process getRef {
val fastqReadError from fastqReadError_getRef
val fastqFileError from fastqFileError_getRef
val seqtypeError from seqtypeError_getRef
val speciesErrorSeqwho from speciesErrorSeqwho_getRef
val speciesError from speciesError_getRef
output:
......@@ -1211,6 +1304,7 @@ process getRef {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
script:
......@@ -1309,6 +1403,7 @@ process alignSampleData {
val fastqReadError from fastqReadError_alignSampleData
val fastqFileError from fastqFileError_alignSampleData
val seqtypeError from seqtypeError_alignSampleData
val speciesErrorSeqwho from speciesErrorSeqwho_alignSampleData
val speciesError from speciesError_alignSampleData
output:
......@@ -1321,6 +1416,7 @@ process alignSampleData {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
script:
......@@ -1374,6 +1470,7 @@ process inferMetadata {
val fastqReadError from fastqReadError_inferMetadata
val fastqFileError from fastqFileError_inferMetadata
val seqtypeError from seqtypeError_inferMetadata
val speciesErrorSeqwho from speciesErrorSeqwho_inferMetadata
val speciesError from speciesError_inferMetadata
output:
......@@ -1385,6 +1482,7 @@ process inferMetadata {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
script:
......@@ -1483,6 +1581,7 @@ process checkMetadata {
val fastqReadError from fastqReadError_checkMetadata
val fastqFileError from fastqFileError_checkMetadata
val seqtypeError from seqtypeError_checkMetadata
val speciesErrorSeqwho from speciesErrorSeqwho_checkMetadata
val speciesError from speciesError_checkMetadata
output:
......@@ -1494,6 +1593,7 @@ process checkMetadata {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
script:
......@@ -1618,6 +1718,7 @@ process alignData {
val fastqReadError from fastqReadError_alignData
val fastqFileError from fastqFileError_alignData
val seqtypeError from seqtypeError_alignData
val speciesErrorSeqwho from speciesErrorSeqwho_alignData
val speciesError from speciesError_alignData
output:
......@@ -1629,6 +1730,7 @@ process alignData {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
script:
......@@ -1695,6 +1797,7 @@ process dedupData {
val fastqReadError from fastqReadError_dedupData
val fastqFileError from fastqFileError_dedupData
val seqtypeError from seqtypeError_dedupData
val speciesErrorSeqwho from speciesErrorSeqwho_dedupData
val speciesError from speciesError_dedupData
val pipelineError from pipelineError_dedupData
......@@ -1708,6 +1811,7 @@ process dedupData {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
pipelineError == "false"
......@@ -1758,6 +1862,7 @@ process makeBigWig {
val fastqReadError from fastqReadError_makeBigWig
val fastqFileError from fastqFileError_makeBigWig
val seqtypeError from seqtypeError_makeBigWig
val speciesErrorSeqwho from speciesErrorSeqwho_makeBigWig
val speciesError from speciesError_makeBigWig
val pipelineError from pipelineError_makeBigWig
......@@ -1769,6 +1874,7 @@ process makeBigWig {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
pipelineError == "false"
......@@ -1802,6 +1908,7 @@ process countData {
val fastqReadError from fastqReadError_countData
val fastqFileError from fastqFileError_countData
val seqtypeError from seqtypeError_countData
val speciesErrorSeqwho from speciesErrorSeqwho_countData
val speciesError from speciesError_countData
val pipelineError from pipelineError_countData
......@@ -1815,6 +1922,7 @@ process countData {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
pipelineError == "false"
......@@ -1889,6 +1997,7 @@ process dataQC {
val fastqReadError from fastqReadError_dataQC
val fastqFileError from fastqFileError_dataQC
val seqtypeError from seqtypeError_dataQC
val speciesErrorSeqwho from speciesErrorSeqwho_dataQC
val speciesError from speciesError_dataQC
val pipelineError from pipelineError_dataQC
......@@ -1902,6 +2011,7 @@ process dataQC {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
pipelineError == "false"
......@@ -1988,6 +2098,7 @@ process aggrQC {
val fastqReadError from fastqReadError_aggrQC
val fastqFileError from fastqFileError_aggrQC
val seqtypeError from seqtypeError_aggrQC
val speciesErrorSeqwho from speciesErrorSeqwho_aggrQC
val speciesError from speciesError_aggrQC
val pipelineError from pipelineError_aggrQC
......@@ -2000,6 +2111,7 @@ process aggrQC {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
pipelineError == "false"
......@@ -2186,6 +2298,7 @@ process uploadExecutionRun {
val fastqReadError from fastqReadError_uploadExecutionRun
val fastqFileError from fastqFileError_uploadExecutionRun
val seqtypeError from seqtypeError_uploadExecutionRun
val speciesErrorSeqwho from speciesErrorSeqwho_uploadExecutionRun
val speciesError from speciesError_uploadExecutionRun
val pipelineError from pipelineError_uploadExecutionRun
......@@ -2198,6 +2311,7 @@ process uploadExecutionRun {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
pipelineError == "false"
......@@ -2301,6 +2415,7 @@ process uploadQC {
val fastqReadError from fastqReadError_uploadQC
val fastqFileError from fastqFileError_uploadQC
val seqtypeError from seqtypeError_uploadQC
val speciesErrorSeqwho from speciesErrorSeqwho_uploadQC
val speciesError from speciesError_uploadQC
val pipelineError from pipelineError_uploadQC
......@@ -2313,6 +2428,7 @@ process uploadQC {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
pipelineError == "false"
......@@ -2381,6 +2497,7 @@ process uploadProcessedFile {
val fastqReadError from fastqReadError_uploadProcessedFile
val fastqFileError from fastqFileError_uploadProcessedFile
val seqtypeError from seqtypeError_uploadProcessedFile
val speciesErrorSeqwho from speciesErrorSeqwho_uploadProcessedFile
val speciesError from speciesError_uploadProcessedFile
val pipelineError from pipelineError_uploadProcessedFile
......@@ -2393,6 +2510,7 @@ process uploadProcessedFile {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
pipelineError == "false"
......@@ -2484,6 +2602,7 @@ process uploadOutputBag {
val fastqReadError from fastqReadError_uploadOutputBag
val fastqFileError from fastqFileError_uploadOutputBag
val seqtypeError from seqtypeError_uploadOutputBag
val speciesErrorSeqwho from speciesErrorSeqwho_uploadOutputBag
val speciesError from speciesError_uploadOutputBag
val pipelineError from pipelineError_uploadOutputBag
......@@ -2496,6 +2615,7 @@ process uploadOutputBag {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
pipelineError == "false"
......@@ -2570,6 +2690,7 @@ process finalizeExecutionRun {
val fastqReadError from fastqReadError_finalizeExecutionRun
val fastqFileError from fastqFileError_finalizeExecutionRun
val seqtypeError from seqtypeError_finalizeExecutionRun
val speciesErrorSeqwho from speciesErrorSeqwho_finalizeExecutionRun
val speciesError from speciesError_finalizeExecutionRun
val pipelineError from pipelineError_finalizeExecutionRun
......@@ -2579,6 +2700,7 @@ process finalizeExecutionRun {
fastqReadError == "false"
fastqFileError == "false"
seqtypeError == "false"
speciesErrorSeqwho == "false"
speciesError == "false"
pipelineError == "false"
......@@ -2611,7 +2733,7 @@ process finalizeExecutionRun {
}
// Combine errors
error_meta = fastqCountError_uploadQC_fail.ifEmpty(false).combine(fastqReadError_uploadQC_fail.ifEmpty(false).combine(fastqFileError_uploadQC_fail.ifEmpty(false).combine(seqtypeError_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(seqtypeError_uploadQC_fail.ifEmpty(false).combine(speciesErrorSeqwho_uploadQC_fail.ifEmpty(false).combine(speciesError_uploadQC_fail.ifEmpty(false).combine(pipelineError_uploadQC_fail.ifEmpty(false)))))))
error_meta. into {
error_failPreExecutionRun
error_uploadQC_fail
......@@ -2630,7 +2752,7 @@ 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 (seqtypeError), val (speciesError), val (pipelineError) from error_failPreExecutionRun
tuple val (fastqCountError), val (fastqReadError), val (fastqFileError), val (seqtypeError), val (speciesErrorSeqwho), val (speciesError), val (pipelineError) from error_failPreExecutionRun
tuple val (fastqCountError_details), val (fastqReadError_details), val (fastqFileError_details), val (seqtypeError_details), val (speciesError_details) from errorDetails
output:
......
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