From b8e8774b9a3082cd90e06b39a93eddde0d69d1f0 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 31 Oct 2020 15:14:13 -0500
Subject: [PATCH] Test failure.
---
workflow/rna-seq.nf | 82 ++++++++++++++++++++++++++-------------------
1 file changed, 48 insertions(+), 34 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index a940778..3099e99 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1,12 +1,12 @@
#!/usr/bin/env nextflow
-// ######## #### ###### ########
-// ## ## ## ## ## ##
-// ## ## ## ## ##
-// ######## ## ## ######
-// ## ## ## ## ##
-// ## ## ## ## ## ##
-// ######## #### ###### ##
+// ######## #### ###### ########
+// ## ## ## ## ## ##
+// ## ## ## ## ##
+// ######## ## ## ######
+// ## ## ## ## ##
+// ## ## ## ## ## ##
+// ######## #### ###### ##
// Define input variables
params.deriva = "${baseDir}/../test_data/auth/credential.json"
@@ -89,7 +89,7 @@ process trackStart {
"""
hostname
ulimit -a
-
+
curl -H 'Content-Type: application/json' -X PUT -d \
'{ \
"sessionId": "${workflow.sessionId}", \
@@ -199,16 +199,16 @@ process getData {
mkdir -p ~/.bdbag
ln -sf `readlink -e deriva-cookies.txt` ~/.bdbag/deriva-cookies.txt
echo -e "LOG: linked" >> ${repRID}.getData.log
-
+
# get bag basename
replicate=\$(basename "${inputBag}" | cut -d "." -f1)
echo -e "LOG: bag replicate name \${replicate}" >> ${repRID}.getData.log
-
+
# unzip bag
echo -e "LOG: unzipping replicate bag" >> ${repRID}.getData.log
unzip ${inputBag}
echo -e "LOG: unzipped" >> ${repRID}.getData.log
-
+
# bag fetch fastq's only and rename by repRID
echo -e "LOG: fetching replicate bdbag" >> ${repRID}.getData.log
sh ${script_bdbagFetch} \${replicate} ${repRID}
@@ -259,7 +259,7 @@ process parseMetadata {
# get experiment RID metadata
exp=\$(python3 ${script_parseMeta} -r ${repRID} -m "${file}" -p expRID)
echo -e "LOG: experiment RID metadata parsed: \${exp}" >> ${repRID}.parseMetadata.log
-
+
# get study RID metadata
study=\$(python3 ${script_parseMeta} -r ${repRID} -m "${file}" -p studyRID)
echo -e "LOG: study RID metadata parsed: \${study}" >> ${repRID}.parseMetadata.log
@@ -267,7 +267,7 @@ process parseMetadata {
# get endedness metadata
endsMeta=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p endsMeta)
echo -e "LOG: endedness metadata parsed: \${endsMeta}" >> ${repRID}.parseMetadata.log
-
+
# ganually get endness
endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${file}" -p endsManual)
echo -e "LOG: endedness manually detected: \${endsManual}" >> ${repRID}.parseMetadata.log
@@ -275,11 +275,11 @@ process parseMetadata {
# get strandedness metadata
stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p stranded)
echo -e "LOG: strandedness metadata parsed: \${stranded}" >> ${repRID}.parseMetadata.log
-
+
# get spike-in metadata
spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p spike)
echo -e "LOG: spike-in metadata parsed: \${spike}" >> ${repRID}.parseMetadata.log
-
+
# get species metadata
species=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experiment}" -p species)
echo -e "LOG: species metadata parsed: \${species}" >> ${repRID}.parseMetadata.log
@@ -358,7 +358,7 @@ process trimData {
fi
echo -e "LOG: trimmed" >> ${repRID}.trimData.log
echo -e "LOG: average trimmed read length: \${readLength}" >> ${repRID}.trimData.log
-
+
# save read length file
echo -e "\${readLength}" > readLength.csv
"""
@@ -381,7 +381,7 @@ getRefInferInput = referenceInfer.combine(deriva_getRefInfer.combine(script_refD
/*
* getRefInfer: dowloads appropriate reference for metadata inference
-*/
+*/
process getRefInfer {
tag "${refName}"
@@ -391,7 +391,7 @@ process getRefInfer {
output:
tuple val (refName), path ("hisat2", type: 'dir'), path ("*.fna"), path ("*.gtf") into refInfer
path ("${refName}", type: 'dir') into bedInfer
-
+
script:
"""
hostname > ${repRID}.${refName}.getRefInfer.log
@@ -532,14 +532,14 @@ process alignSampleData {
echo -e "LOG: aligning ${ends}" >> ${repRID}.${ref}.alignSampleData.log
if [ "${ends}" == "se" ]
then
-
+
hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome -U ${fastq1} --summary-file ${ref}.alignSampleSummary.txt --new-summary
elif [ "${ends}" == "pe" ]
then
hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome --no-mixed --no-discordant -1 ${fastq1} -2 ${fastq2} --summary-file ${ref}.alignSampleSummary.txt --new-summary
fi
echo -e "LOG: aliged" >> ${repRID}.${ref}.alignSampleData.log
-
+
# convert the output sam file to a sorted bam file using Samtools
echo -e "LOG: converting from sam to bam" >> ${repRID}.${ref}.alignSampleData.log
samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${ref}.sampled.bam ${ref}.sampled.sam
@@ -639,7 +639,7 @@ process inferMetadata {
ended=`bash inferMeta.sh endness ${repRID}.infer_experiment.txt`
fail=`bash inferMeta.sh fail ${repRID}.infer_experiment.txt`
- if [ \${ended} == "PairEnd" ]
+ if [ \${ended} == "PairEnd" ]
then
ends="pe"
percentF=`bash inferMeta.sh pef ${repRID}.infer_experiment.txt`
@@ -728,7 +728,7 @@ process getRef {
output:
tuple path ("hisat2", type: 'dir'), path ("bed", type: 'dir'), path ("*.fna"), path ("*.gtf"), path ("geneID.tsv"), path ("Entrez.tsv") into reference
-
+
script:
"""
hostname > ${repRID}.getRef.log
@@ -847,7 +847,7 @@ process alignData {
strandedParam="--rna-strandness R"
elif [ "${stranded}" == "reverse" ] && [ "${ends}" == "pe" ]
then
- strandedParam="--rna-strandness RF"
+ strandedParam="--rna-strandness RF"
fi
# align the reads with Hisat2
@@ -860,7 +860,7 @@ process alignData {
hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome \${strandedParam} --no-mixed --no-discordant -1 ${fastq[0]} -2 ${fastq[1]} --summary-file ${repRID}.alignSummary.txt --new-summary
fi
echo -e "LOG: alignined" >> ${repRID}.align.log
-
+
# convert the output sam file to a sorted bam file using Samtools
echo -e "LOG: converting from sam to bam" >> ${repRID}.align.log
samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${repRID}.bam ${repRID}.sam
@@ -892,7 +892,7 @@ process dedupData {
output:
tuple path ("${repRID}.sorted.deduped.bam"), path ("${repRID}.sorted.deduped.bam.bai") into dedupBam
- tuple path ("${repRID}.sorted.deduped.*.bam"), path ("${repRID}.sorted.deduped.*.bam.bai") into dedupChrBam
+ tuple path ("${repRID}.sorted.deduped.*.bam"), path ("${repRID}.sorted.deduped.*.bam.bai") into dedupChrBam
path ("*.deduped.Metrics.txt") into dedupQC
script:
@@ -908,7 +908,7 @@ process dedupData {
# sort the bam file using Samtools
echo -e "LOG: sorting the bam file" >> ${repRID}.dedup.log
samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.deduped.bam ${repRID}.deduped.bam
-
+
# index the sorted bam using Samtools
echo -e "LOG: indexing sorted bam file" >> ${repRID}.dedup.log
samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bam.bai
@@ -1004,7 +1004,7 @@ process countData {
featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o ${repRID}.countData -s \${stranding} -p -B -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam
fi
echo -e "LOG: counted" >> ${repRID}.countData.log
-
+
# extract assigned reads
grep -m 1 'Assigned' *.countData.summary | grep -oe '\\([0-9.]*\\)' > assignedReads.csv
@@ -1069,12 +1069,12 @@ process dataQC {
tuple path (bam), path (bai) from dedupBam_dataQC
tuple path (chrBam), path (chrBai) from dedupChrBam
val ends from endsInfer_dataQC
-
+
output:
path "${repRID}.tin.hist.tsv" into tinHist
path "${repRID}.tin.med.csv" into inferMetadata_tinMed
path "${repRID}.insertSize.inner_distance_freq.txt" into innerDistance
-
+
script:
"""
hostname > ${repRID}.dataQC.log
@@ -1179,8 +1179,8 @@ process aggrQC {
echo -e "LOG: creating run table" >> ${repRID}.aggrQC.log
echo -e "Session\tSession ID\tStart Time\tPipeline Version\tInput" > run.tsv
echo -e "Session\t${workflow.sessionId}\t${workflow.start}\t${workflow.manifest.version}\t\${input}" >> run.tsv
-
-
+
+
# make RID table
echo -e "LOG: creating RID table" >> ${repRID}.aggrQC.log
echo -e "Replicate\tReplicate RID\tExperiment RID\tStudy RID" > rid.tsv
@@ -1224,11 +1224,11 @@ process aggrQC {
process outputBag {
tag "${repRID}"
publishDir "${outDir}/outputBag", mode: 'copy', pattern: "Replicate_${repRID}.outputBag.zip"
-
+
input:
path multiqc
path multiqcJSON
-
+
output:
path ("Replicate_*.zip") into outputBag
@@ -1239,4 +1239,18 @@ process outputBag {
cp ${multiqcJSON} Replicate_${repRID}.outputBag
bdbag Replicate_${repRID}.outputBag --archiver zip
"""
-}
\ No newline at end of file
+}
+
+workflow.onError = {
+ def msg = """\
+
+ Pipeline error summary
+ ---------------------------
+ RID : ${params.repRID}
+ Message : ${workflow.errorMessage}
+ exit status : ${workflow.exitStatus}
+ """
+ .stripIndent()
+
+ sendMail(to: 'venkat.malladi@utsouthwestern.edu', subject: 'GUDMAP RNA-seq error execution', body: msg)
+}
--
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