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Commit 2c368957 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add ambiguous species error reporting

parent e7c1ae2a
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2 merge requests!58Develop,!56Resolve "Detect error in inferMetadata for tracking"
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workflow/rna-seq.nf
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...@@ -772,6 +772,7 @@ process inferMetadata { ...@@ -772,6 +772,7 @@ process inferMetadata {
output: output:
path "infer.csv" into inferMetadata_fl path "infer.csv" into inferMetadata_fl
path "${repRID}.infer_experiment.txt" into inferExperiment path "${repRID}.infer_experiment.txt" into inferExperiment
path "speciesError.csv" into speciesError_fl
when: when:
fastqCountError_inferMetadata == "false" fastqCountError_inferMetadata == "false"
...@@ -802,6 +803,7 @@ process inferMetadata { ...@@ -802,6 +803,7 @@ process inferMetadata {
fi fi
echo -e "LOG: inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log echo -e "LOG: inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log
speciesError=false
# determine species # determine species
if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 40)) ] if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 40)) ]
then then
...@@ -817,7 +819,8 @@ process inferMetadata { ...@@ -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 echo -e "LOG: ERROR - inference of species returns an ambiguous result: hu=\${align_hu} mo=\${align_mo}" >> ${repRID}.inferMetadata.log
if [ "${speciesForce}" == "" ] if [ "${speciesForce}" == "" ]
then then
exit 1 speciesError=true
speciesError_details="**Inference of species returns an ambiguous result:** Percent aligned to human = \${align_hu}, percent aligned to mouse = \${align_mo}"
fi fi
fi fi
if [ "${speciesForce}" != "" ] if [ "${speciesForce}" != "" ]
...@@ -869,6 +872,9 @@ process inferMetadata { ...@@ -869,6 +872,9 @@ process inferMetadata {
# write inferred metadata to file # write inferred metadata to file
echo "\${ends},\${stranded},\${spike},\${species},\${align_ercc},\${align_hu},\${align_mo},\${percentF},\${percentR},\${fail}" 1>> infer.csv 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 { ...@@ -930,6 +936,32 @@ speciesInfer.into {
speciesInfer_failExecutionRun 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 * checkMetadata: checks the submitted metada against inferred
*/ */
...@@ -947,6 +979,7 @@ process checkMetadata { ...@@ -947,6 +979,7 @@ process checkMetadata {
val speciesInfer from speciesInfer_checkMetadata val speciesInfer from speciesInfer_checkMetadata
val fastqCountError_checkMetadata val fastqCountError_checkMetadata
val fastqReadError_checkMetadata val fastqReadError_checkMetadata
val speciesError_checkMetadata
output: output:
path ("check.csv") into checkMetadata_fl path ("check.csv") into checkMetadata_fl
...@@ -955,6 +988,7 @@ process checkMetadata { ...@@ -955,6 +988,7 @@ process checkMetadata {
when: when:
fastqCountError_checkMetadata == "false" fastqCountError_checkMetadata == "false"
fastqReadError_checkMetadata == "false" fastqReadError_checkMetadata == "false"
speciesError_checkMetadata == "false"
script: script:
""" """
...@@ -1136,6 +1170,7 @@ process uploadExecutionRun { ...@@ -1136,6 +1170,7 @@ process uploadExecutionRun {
val inputBagRID from inputBagRID_uploadExecutionRun val inputBagRID from inputBagRID_uploadExecutionRun
val fastqCountError_uploadExecutionRun val fastqCountError_uploadExecutionRun
val fastqReadError_uploadExecutionRun val fastqReadError_uploadExecutionRun
val speciesError_uploadExecutionRun
output: output:
path ("executionRunRID.csv") into executionRunRID_fl path ("executionRunRID.csv") into executionRunRID_fl
...@@ -1144,6 +1179,7 @@ process uploadExecutionRun { ...@@ -1144,6 +1179,7 @@ process uploadExecutionRun {
upload upload
fastqCountError_uploadExecutionRun == "false" fastqCountError_uploadExecutionRun == "false"
fastqReadError_uploadExecutionRun == "false" fastqReadError_uploadExecutionRun == "false"
speciesReadError_uploadExecutionRun == "false"
script: script:
""" """
...@@ -1222,6 +1258,7 @@ process getRef { ...@@ -1222,6 +1258,7 @@ process getRef {
val species from speciesInfer_getRef val species from speciesInfer_getRef
val fastqCountError_getRef val fastqCountError_getRef
val fastqReadError_getRef val fastqReadError_getRef
val speciesError_getRef
val pipelineError_getRef val pipelineError_getRef
output: output:
...@@ -1230,6 +1267,7 @@ process getRef { ...@@ -1230,6 +1267,7 @@ process getRef {
when: when:
fastqCountError_getRef == "false" fastqCountError_getRef == "false"
fastqReadError_getRef == "false" fastqReadError_getRef == "false"
speciesError_getRef == "false"
pipelineError_getRef == "false" pipelineError_getRef == "false"
script: script:
...@@ -1320,6 +1358,7 @@ process alignData { ...@@ -1320,6 +1358,7 @@ process alignData {
val stranded from strandedInfer_alignData val stranded from strandedInfer_alignData
val fastqCountError_alignData val fastqCountError_alignData
val fastqReadError_alignData val fastqReadError_alignData
val speciesError_alignData
val pipelineError_alignData val pipelineError_alignData
output: output:
...@@ -1329,6 +1368,7 @@ process alignData { ...@@ -1329,6 +1368,7 @@ process alignData {
when: when:
fastqCountError_alignData == "false" fastqCountError_alignData == "false"
fastqReadError_alignData == "false" fastqReadError_alignData == "false"
speciesError_alignData == "false"
pipelineError_alignData == "false" pipelineError_alignData == "false"
script: script:
...@@ -1395,6 +1435,7 @@ process dedupData { ...@@ -1395,6 +1435,7 @@ process dedupData {
tuple path (bam), path (bai) from rawBam_dedupData tuple path (bam), path (bai) from rawBam_dedupData
val fastqCountError_dedupData val fastqCountError_dedupData
val fastqReadError_dedupData val fastqReadError_dedupData
val speciesError_dedupData
val pipelineError_dedupData val pipelineError_dedupData
output: output:
...@@ -1405,6 +1446,7 @@ process dedupData { ...@@ -1405,6 +1446,7 @@ process dedupData {
when: when:
fastqCountError_dedupData == 'false' fastqCountError_dedupData == 'false'
fastqReadError_dedupData == 'false' fastqReadError_dedupData == 'false'
speciesError_dedupData == 'false'
pipelineError_dedupData == 'false' pipelineError_dedupData == 'false'
script: script:
...@@ -1452,6 +1494,7 @@ process makeBigWig { ...@@ -1452,6 +1494,7 @@ process makeBigWig {
tuple path (bam), path (bai) from dedupBam_makeBigWig tuple path (bam), path (bai) from dedupBam_makeBigWig
val fastqCountError_makeBigWig val fastqCountError_makeBigWig
val fastqReadError_makeBigWig val fastqReadError_makeBigWig
val speciesError_makeBigWig
val pipelineError_makeBigWig val pipelineError_makeBigWig
output: output:
...@@ -1460,6 +1503,7 @@ process makeBigWig { ...@@ -1460,6 +1503,7 @@ process makeBigWig {
when: when:
fastqCountError_makeBigWig == 'false' fastqCountError_makeBigWig == 'false'
fastqReadError_makeBigWig == 'false' fastqReadError_makeBigWig == 'false'
speciesError_makeBigWig == 'false'
pipelineError_makeBigWig == 'false' pipelineError_makeBigWig == 'false'
script: script:
...@@ -1490,6 +1534,7 @@ process countData { ...@@ -1490,6 +1534,7 @@ process countData {
val stranded from strandedInfer_countData val stranded from strandedInfer_countData
val fastqCountError_countData val fastqCountError_countData
val fastqReadError_countData val fastqReadError_countData
val speciesError_countData
val pipelineError_countData val pipelineError_countData
output: output:
...@@ -1500,6 +1545,7 @@ process countData { ...@@ -1500,6 +1545,7 @@ process countData {
when: when:
fastqCountError_countData == 'false' fastqCountError_countData == 'false'
fastqReadError_countData == 'false' fastqReadError_countData == 'false'
speciesError_countData == 'false'
pipelineError_countData == 'false' pipelineError_countData == 'false'
script: script:
...@@ -1569,6 +1615,7 @@ process fastqc { ...@@ -1569,6 +1615,7 @@ process fastqc {
path (fastq) from fastqs_fastqc path (fastq) from fastqs_fastqc
val fastqCountError_fastqc val fastqCountError_fastqc
val fastqReadError_fastqc val fastqReadError_fastqc
val speciesError_fastqc
val pipelineError_fastqc val pipelineError_fastqc
output: output:
...@@ -1578,6 +1625,7 @@ process fastqc { ...@@ -1578,6 +1625,7 @@ process fastqc {
when: when:
fastqCountError_fastqc == 'false' fastqCountError_fastqc == 'false'
fastqReadError_fastqc == 'false' fastqReadError_fastqc == 'false'
speciesError_fastqc == 'false'
pipelineError_fastqc == 'false' pipelineError_fastqc == 'false'
script: script:
...@@ -1620,6 +1668,7 @@ process dataQC { ...@@ -1620,6 +1668,7 @@ process dataQC {
val ends from endsInfer_dataQC val ends from endsInfer_dataQC
val fastqCountError_dataQC val fastqCountError_dataQC
val fastqReadError_dataQC val fastqReadError_dataQC
val speciesError_dataQC
val pipelineError_dataQC val pipelineError_dataQC
output: output:
...@@ -1630,6 +1679,7 @@ process dataQC { ...@@ -1630,6 +1679,7 @@ process dataQC {
when: when:
fastqCountError_dataQC == 'false' fastqCountError_dataQC == 'false'
fastqReadError_dataQC == 'false' fastqReadError_dataQC == 'false'
speciesError_dataQC == 'false'
pipelineError_dataQC == 'false' pipelineError_dataQC == 'false'
script: script:
...@@ -1708,6 +1758,7 @@ process aggrQC { ...@@ -1708,6 +1758,7 @@ process aggrQC {
val expRID from expRID_aggrQC val expRID from expRID_aggrQC
val fastqCountError_aggrQC val fastqCountError_aggrQC
val fastqReadError_aggrQC val fastqReadError_aggrQC
val speciesError_aggrQC
val pipelineError_aggrQC val pipelineError_aggrQC
output: output:
...@@ -1717,6 +1768,7 @@ process aggrQC { ...@@ -1717,6 +1768,7 @@ process aggrQC {
when: when:
fastqCountError_aggrQC == 'false' fastqCountError_aggrQC == 'false'
fastqReadError_aggrQC == 'false' fastqReadError_aggrQC == 'false'
speciesError_aggrQC == 'false'
pipelineError_aggrQC == 'false' pipelineError_aggrQC == 'false'
script: script:
...@@ -1803,6 +1855,7 @@ process uploadQC { ...@@ -1803,6 +1855,7 @@ process uploadQC {
val finalCount from assignedReadsInfer_uploadQC val finalCount from assignedReadsInfer_uploadQC
val fastqCountError_uploadQC val fastqCountError_uploadQC
val fastqReadError_uploadQC val fastqReadError_uploadQC
val speciesError_uploadQC
val pipelineError_uploadQC val pipelineError_uploadQC
output: output:
...@@ -1812,6 +1865,7 @@ process uploadQC { ...@@ -1812,6 +1865,7 @@ process uploadQC {
upload upload
fastqCountError_uploadQC == 'false' fastqCountError_uploadQC == 'false'
fastqReadError_uploadQC == 'false' fastqReadError_uploadQC == 'false'
speciesError_uploadQC == 'false'
pipelineError_uploadQC == 'false' pipelineError_uploadQC == 'false'
script: script:
...@@ -1877,6 +1931,7 @@ process uploadProcessedFile { ...@@ -1877,6 +1931,7 @@ process uploadProcessedFile {
val executionRunRID from executionRunRID_uploadProcessedFile val executionRunRID from executionRunRID_uploadProcessedFile
val fastqCountError_uploadProcessedFile val fastqCountError_uploadProcessedFile
val fastqReadError_uploadProcessedFile val fastqReadError_uploadProcessedFile
val speciesError_uploadProcessedFile
val pipelineError_uploadProcessedFile val pipelineError_uploadProcessedFile
output: output:
...@@ -1886,6 +1941,7 @@ process uploadProcessedFile { ...@@ -1886,6 +1941,7 @@ process uploadProcessedFile {
upload upload
fastqCountError_uploadProcessedFile == 'false' fastqCountError_uploadProcessedFile == 'false'
fastqReadError_uploadProcessedFile == 'false' fastqReadError_uploadProcessedFile == 'false'
speciesError_uploadProcessedFile == 'false'
pipelineError_uploadProcessedFile == 'false' pipelineError_uploadProcessedFile == 'false'
script: script:
...@@ -1967,6 +2023,7 @@ process uploadOutputBag { ...@@ -1967,6 +2023,7 @@ process uploadOutputBag {
val executionRunRID from executionRunRID_uploadOutputBag val executionRunRID from executionRunRID_uploadOutputBag
val fastqCountError_uploadOutputBag val fastqCountError_uploadOutputBag
val fastqReadError_uploadOutputBag val fastqReadError_uploadOutputBag
val speciesError_uploadOutputBag
val pipelineError_uploadOutputBag val pipelineError_uploadOutputBag
output: output:
...@@ -1976,6 +2033,7 @@ process uploadOutputBag { ...@@ -1976,6 +2033,7 @@ process uploadOutputBag {
upload upload
fastqCountError_uploadOutputBag == 'false' fastqCountError_uploadOutputBag == 'false'
fastqReadError_uploadOutputBag == 'false' fastqReadError_uploadOutputBag == 'false'
speciesError_uploadOutputBag == 'false'
pipelineError_uploadOutputBag == 'false' pipelineError_uploadOutputBag == 'false'
script: script:
...@@ -2069,9 +2127,12 @@ process failPreExecutionRun { ...@@ -2069,9 +2127,12 @@ process failPreExecutionRun {
val fastqCountError_details val fastqCountError_details
val fastqReadError from fastqReadError_failPreExecutionRun val fastqReadError from fastqReadError_failPreExecutionRun
val fastqReadError_details val fastqReadError_details
val speciesError from speciesError_failPreExecutionRun
val speciesError_details
when: when:
upload upload
fastqCountError == 'true' || fastqReadError == 'true' fastqCountError == 'true' || fastqReadError == 'true' || speciesError == 'true'
script: script:
""" """
...@@ -2085,6 +2146,9 @@ process failPreExecutionRun { ...@@ -2085,6 +2146,9 @@ process failPreExecutionRun {
elif [ ${fastqReadError} == true ] elif [ ${fastqReadError} == true ]
then then
errorDetails=\$(echo \$(errorDetails)${fastqReadError_details}"\\n") errorDetails=\$(echo \$(errorDetails)${fastqReadError_details}"\\n")
elif [ ${speciesError} == true ]
then
errorDetails=\$(echo \$(errorDetails)${speciesError_details}"\\n")
fi fi
echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun.log echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun.log
......
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