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Commit 03aa79a9 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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3 merge requests!37v0.0.1,!24Develop,!22Resolve "process_count"
Pipeline #6279 passed with stages
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.gitlab-ci.yml
+ 14
− 8
View file @ 03aa79a9
before_script:
- module add python/3.6.1-2-anaconda
- module add python/3.6.4-anaconda
- pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
- module load singularity/3.0.2
- module load nextflow/19.09.0
......@@ -22,8 +22,8 @@ getData:
stage: unit
script:
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- unzip ./test_data/bagit/Replicate_16-1ZX4
- singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4
- unzip ./test_data/bagit/Study_Q-Y4H0.zip
- singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' bash ./workflow/scripts/bdbagFetch.sh Study_Q-Y4H0 Q-Y4H0 TEST
- pytest -m getData
parseMetadata:
......@@ -53,14 +53,14 @@ trimData:
alignData:
stage: unit
script:
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz --summary-file ${repRID}.alignSummary.txt --new-summary
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.se.bam Q-Y5JA_1M.se.sam
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.bam
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bai
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.pe.unal.gz -S Q-Y5JA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5JA_1M_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5JA_1M_R2_val_2.fq.gz
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bam.bai
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.pe.unal.gz -S Q-Y5JA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5JA_1M_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5JA_1M_R2_val_2.fq.gz --summary-file ${repRID}.alignSummary.txt --new-summary
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.pe.bam Q-Y5JA_1M.pe.sam
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.bam
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.sorted.bai
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.sorted.bam.bai
- pytest -m alignData
dedupData:
......@@ -68,7 +68,7 @@ dedupData:
script:
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam Q-Y5JA_1M.se.sorted.deduped.bai
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam Q-Y5JA_1M.se.sorted.deduped.bam.bai
- pytest -m dedupData
makeBigWig:
......@@ -90,6 +90,12 @@ fastqc:
- singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz -o .
- pytest -m fastqc
inferMetadata:
stage: unit
script:
- singularity run 'docker://bicf/rseqc3.0:2.0.0' tin.py -i ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed
- pytest -m inferMetadata
integration_se:
stage: integration
script:
......
docs/RNA-Seq Pipeline Design Flowchart.drawio
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id="74e2e168-ea6b-b213-b513-2b3c1d86103e">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</diagram></mxfile>
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workflow/conf/biohpc.config
+ 4
− 1
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......@@ -24,7 +24,10 @@ process {
withName: dedupData {
queue = 'super'
}
withName: fastqc {
withName:fastqc {
queue = 'super'
}
withName:inferMetadata {
queue = 'super'
}
withName: makeBigWig {
......
workflow/nextflow.config
+ 8
− 5
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......@@ -17,13 +17,13 @@ process {
withName:getData {
container = 'bicf/gudmaprbkfilexfer:1.3'
}
withName:parseMetadata {
withName: parseMetadata {
container = 'bicf/python3:1.3'
}
withName:getRef {
withName: getRef {
container = 'bicf/awscli:1.1'
}
withName:trimData {
withName: trimData {
container = 'bicf/trimgalore:1.1'
}
withName: alignData {
......@@ -32,11 +32,14 @@ process {
withName: dedupData {
container = 'bicf/gudmaprbkdedup:2.0.0'
}
withName: makeBigWig {
container = 'bicf/deeptools3.3:2.0.0'
}
withName: fastqc {
container = 'bicf/fastqc:2.0.0'
}
withName: makeBigWig {
container = 'bicf/deeptools3.3:2.0.0'
withName:inferMetadata{
container = 'bicf/rseqc3.0:2.0.0'
}
withName: makeFeatureCounts {
container = 'bicf/subread2:2.0.0'
......
workflow/rna-seq.nf 100755 → 100644
+ 118
− 30
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......@@ -39,6 +39,7 @@ referenceBase = "/project/BICF/BICF_Core/shared/gudmap/references"
script_bdbagFetch = Channel.fromPath("${baseDir}/scripts/bdbagFetch.sh")
script_parseMeta = Channel.fromPath("${baseDir}/scripts/parseMeta.py")
script_calculateTPM = Channel.fromPath("${baseDir}/scripts/calculateTPM.R")
script_inferMeta = Channel.fromPath("${baseDir}/scripts/inferMeta.sh")
/*
* splitData: split bdbag files by replicate so fetch can occure in parallel, and rename files to replicate rid
......@@ -113,7 +114,7 @@ process getData {
"""
}
// Split fastq's
// Replicate raw fastqs for multiple process inputs
fastqs.into {
fastqs_trimData
fastqs_fastqc
......@@ -185,6 +186,7 @@ metadata.splitCsv(sep: ",", header: false).separate(
spike,
species
)
// Replicate metadata for multiple process inputs
endsManual.into {
endsManual_trimData
endsManual_alignData
......@@ -212,9 +214,7 @@ process getRef {
val species_getRef
output:
path ("hisat2") type 'dir' into reference
path ("bed") type 'dir' into bedFile
tuple val ("${refRID}"), path ("genome.fna"), path ("genome.gtf") into featureCountsRef
path ("*") into reference
script:
"""
......@@ -257,6 +257,13 @@ process getRef {
"""
}
// Replicate reference for multiple process inputs
reference.into {
reference_alignData
reference_makeFeatureCounts
reference_inferMeta
}
/*
* trimData: trims any adapter or non-host sequences from the data
*/
......@@ -270,6 +277,7 @@ process trimData {
output:
path ("*.fq.gz") into fastqs_trimmed
path ("*_trimming_report.txt") into trimQC
path ("${repRID}.trimData.log")
path ("${repRID}.trimData.err")
......@@ -289,10 +297,6 @@ process trimData {
"""
}
reference.into {
reference_alignData
}
/*
* alignData: aligns the reads to a reference database
*/
......@@ -307,8 +311,8 @@ process alignData {
path reference_alignData
output:
path ("${repRID}.sorted.bam") into rawBam
path ("${repRID}.sorted.bai") into rawBai
tuple val ("${repRID}"), path ("${repRID}.sorted.bam"), path ("${repRID}.sorted.bam.bai") into rawBam
path ("*.alignSummary.txt") into alignQC
path ("${repRID}.align.out")
path ("${repRID}.align.err")
......@@ -320,19 +324,24 @@ process alignData {
# align reads
if [ "${endsManual_alignData}" == "se" ]
then
hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} -U ${fastq[0]} 1>${repRID}.align.out 2>${repRID}.align.err
hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} -U ${fastq[0]} --summary-file ${repRID}.alignSummary.txt --new-summary 1>${repRID}.align.out 2>${repRID}.align.err
elif [ "${endsManual_alignData}" == "pe" ]
then
hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} --no-mixed --no-discordant -1 ${fastq[0]} -2 ${fastq[1]} 1>${repRID}.align.out 2>${repRID}.align.err
hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} --no-mixed --no-discordant -1 ${fastq[0]} -2 ${fastq[1]} --summary-file ${repRID}.alignSummary.txt --new-summary 1>${repRID}.align.out 2>${repRID}.align.err
fi
# convert sam to bam and sort and index
samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${repRID}.bam ${repRID}.sam 1>>${repRID}.align.out 2>>${repRID}.align.err;
samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.bam ${repRID}.bam 1>>${repRID}.align.out 2>>${repRID}.align.err;
samtools index -@ `nproc` -b ${repRID}.sorted.bam ${repRID}.sorted.bai 1>>${repRID}.align.out 2>>${repRID}.align.err;
samtools index -@ `nproc` -b ${repRID}.sorted.bam ${repRID}.sorted.bam.bai 1>>${repRID}.align.out 2>>${repRID}.align.err;
"""
}
// Replicate rawBam for multiple process inputs
rawBam.into {
rawBam_dedupData
}
/*
*dedupData: mark the duplicate reads, specifically focused on PCR or optical duplicates
*/
......@@ -342,11 +351,11 @@ process dedupData {
publishDir "${logsDir}", mode: 'copy', pattern: "*.dedup.{out,err}"
input:
path rawBam
set val (repRID), path (inBam), path (inBai) from rawBam_dedupData
output:
tuple val ("${repRID}"), path ("${repRID}.sorted.deduped.bam"), path ("${repRID}.sorted.deduped.bai") into dedupBam
tuple val ("${repRID}"), path ("${repRID}.sorted.deduped.bam"), path ("${repRID}.sorted.deduped.bai") into featureCountsIn
tuple val ("${repRID}"), path ("${repRID}.sorted.deduped.bam"), path ("${repRID}.sorted.deduped.bam.bai") into dedupBam
path ("*.deduped.Metrics.txt") into dedupQC
path ("${repRID}.dedup.out")
path ("${repRID}.dedup.err")
......@@ -356,21 +365,28 @@ process dedupData {
ulimit -a >>${repRID}.dedup.err
# remove duplicated reads
java -jar /picard/build/libs/picard.jar MarkDuplicates I=${rawBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
java -jar /picard/build/libs/picard.jar MarkDuplicates I=${inBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.deduped.bam ${repRID}.deduped.bam 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bai 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bam.bai 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
"""
}
// Replicate dedup bam/bai for multiple process inputs
dedupBam.into {
dedupBam_makeFeatureCounts
dedupBam_makeBigWig
dedupBam_inferMeta
}
/*
*makeBigWig: make bigwig file
*Make BigWig files for output
*/
process makeBigWig {
tag "${repRID}"
publishDir "${logsDir}", mode: 'copy', pattern: "*.makeBigWig.err"
input:
tuple val (repRID), path (inBam), path (inBai) from dedupBam
set val (repRID), path (inBam), path (inBai) from dedupBam_makeBigWig
output:
path ("${repRID}.bw")
......@@ -386,30 +402,32 @@ process makeBigWig {
*/
process makeFeatureCounts {
tag "${repRID}"
publishDir "${outDir}/featureCounts", mode: 'copy', pattern: "${repRID}*.featureCounts*"
publishDir "${outDir}/featureCounts", mode: 'copy', pattern: "${repRID}*.countTable.csv"
publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.makeFetureCounts.{out,err}"
input:
path script_calculateTPM
tuple val (repRID1), path (bam), path (bai) from featureCountsIn
tuple val (repRID2), path (genome), path (gtf) from featureCountsRef
tuple val (repRID), path (bam), path (bai) from dedupBam_makeFeatureCounts
path reference_makeFeatureCounts
val endsManual_featureCounts
output:
tuple val ("${repRID}"), path ("${repRID}.featureCounts.summary"), path ("${repRID}.featureCounts"), path ("${bam}.featureCounts.sam") into featureCountsOut
path ("*.countTable.csv") into counts
path ("*.featureCounts.summary") into countsQC
script:
"""
if [ "${endsManual_featureCounts }" == "se" ]; then
featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -a ${gtf} -o ${repRID}.featureCounts -g 'gene_name' ${repRID}.sorted.deduped.bam;
elif [ "${endsManual_featureCounts }" == "pe" ]; then
featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -p -a ${gtf} -o ${repRID}.featureCounts -g 'gene_name' ${repRID}.sorted.deduped.bam;
fi;
if [ "${endsManual_featureCounts }" == "se" ]
then
featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s 1 -a ./genome.gtf -o ${repRID}.featureCounts -g 'gene_name' ${repRID}.sorted.deduped.bam;
elif [ "${endsManual_featureCounts }" == "pe" ]
then
featureCounts -R SAM -p -G ./genmome.fna -T `nproc` -s 1 -p -a ./genome.gtf -o ${repRID}.featureCounts -g 'gene_name' ${repRID}.sorted.deduped.bam;
fi
Rscript calculateTPM.R --count "${repRID}.featureCounts";
"""
}
/*
*fastqc: run fastqc on untrimmed fastq's
*/
......@@ -433,3 +451,73 @@ process fastqc {
fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
"""
}
/*
*inferMetadata: run RSeQC to collect stats and infer experimental metadata
*/
process inferMetadata {
tag "${repRID}"
publishDir "${logsDir}", mode: 'copy', pattern: "*.rseqc.err"
input:
path script_inferMeta
path reference_inferMeta
set val (repRID), path (inBam), path (inBai) from dedupBam_inferMeta
output:
path "infer.csv" into inferedMetadata
path "${inBam.baseName}.tin.xls" into tin
path "${repRID}.insertSize.inner_distance_freq.txt" optional true into innerDistance
script:
"""
hostname >${repRID}.rseqc.err
ulimit -a >>${repRID}.rseqc.err
# infer experimental setting from dedup bam
infer_experiment.py -r ./bed/genome.bed -i "${inBam}" >${repRID}.rseqc.log
endness=`bash inferMeta.sh endness ${repRID}.rseqc.log`
fail=`bash inferMeta.sh fail ${repRID}.rseqc.log`
if [ \${endness} == "PairEnd" ]
then
percentF=`bash inferMeta.sh pef ${repRID}.rseqc.log`
percentR=`bash inferMeta.sh per ${repRID}.rseqc.log`
inner_distance.py -i "${inBam}" -o ${repRID}.insertSize -r ./bed/genome.bed
elif [ \${endness} == "SingleEnd" ]
then
percentF=`bash inferMeta.sh sef ${repRID}.rseqc.log`
percentR=`bash inferMeta.sh ser ${repRID}.rseqc.log`
fi
if [ \$percentF -gt 0.25 ] && [ \$percentR -lt 0.25 ]
then
stranded="forward"
if [ \$endness == "PairEnd" ]
then
strategy="1++,1--,2+-,2-+"
else
strategy="++,--"
fi
elif [ \$percentR -gt 0.25 ] && [ \$percentF -lt 0.25 ]
then
stranded="reverse"
if [ \$endness == "PairEnd" ]
then
strategy="1+-,1-+,2++,2--"
else
strategy="+-,-+"
fi
else
stranded="unstranded"
strategy="us"
fi
# calcualte TIN values per feature
tin.py -i "${inBam}" -r ./bed/genome.bed
# write infered metadata to file
echo \${endness},\${stranded},\${strategy},\${percentF},\${percentR},\${fail} > infer.csv
"""
}
\ No newline at end of file
workflow/scripts/bdbagFetch.sh
+ 12
− 5
View file @ 03aa79a9
#!/bin/bash
bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz $1
for i in $(find */ -name "*.R*.fastq.gz"); do
path=${2}$(echo ${i##*/} | grep -o "\.R.\.fastq\.gz");
mv ${i} ./${path}
done;
\ No newline at end of file
if [ -z "${3}" ]
then
bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
for i in $(find */ -name "*.R*.fastq.gz")
do
path=${2}$(echo ${i##*/} | grep -o "\.R.\.fastq\.gz")
mv ${i} ./${path}
done
elif [ "${3}" == "TEST" ]
then
bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}
fi
\ No newline at end of file
workflow/scripts/inferMeta.sh 0 → 100644
+ 21
− 0
View file @ 03aa79a9
#!/bin/bash
if [ "${1}" == "endness" ]
then
awk '/Data/ {print}' "${2}" | sed -e 's/^This is //' -e 's/ Data$//'
elif [ "${1}" == "fail" ]
then
awk '/Fraction of reads failed/ {print}' "${2}" | sed -e 's/^Fraction of reads failed to determine: //'
elif [ "${1}" == "sef" ]
then
awk '/\+\+,--/ {print}' "${2}" | sed -e 's/^Fraction of reads explained by "++,--": //'
elif [ "${1}" == "ser" ]
then
awk '/\+-,-\+/ {print}' "${2}" | sed -e 's/^Fraction of reads explained by "+-,-+": //'
elif [ "${1}" == "pef" ]
then
awk '/1\+\+,1--,2\+-,2-\+/ {print}' "${2}" | sed -e 's/^Fraction of reads explained by "1++,1--,2+-,2-+": //'
elif [ "${1}" == "per" ]
then
awk '/1\+-,1-\+,2\+\+,2--/ {print}' "${2}" | sed -e 's/^Fraction of reads explained by "1+-,1-+,2++,2--": //'
fi
\ No newline at end of file
workflow/tests/test_alignReads.py
+ 2
− 2
View file @ 03aa79a9
......@@ -13,11 +13,11 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
def test_alignData_se():
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.unal.gz'))
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.bam'))
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.bai'))
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.bam.bai'))
@pytest.mark.alignData
def test_alignData_pe():
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.unal.gz'))
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.sorted.bam'))
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.sorted.bai'))
\ No newline at end of file
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.sorted.bam.bai'))
workflow/tests/test_dedupReads.py
+ 2
− 1
View file @ 03aa79a9
......@@ -11,4 +11,5 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.dedupData
def test_dedupData():
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.deduped.bam'))
\ No newline at end of file
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.bam'))
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.bam.bai'))
workflow/tests/test_getData.py
+ 2
− 2
View file @ 03aa79a9
......@@ -10,5 +10,5 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.getData
def test_getData():
assert os.path.exists(os.path.join(test_output_path, 'Replicate_16-1ZX4/bagit.txt'))
assert os.path.exists(os.path.join(test_output_path, '16-1ZX4.R1.fastq.gz'))
\ No newline at end of file
assert os.path.exists(os.path.join(test_output_path, 'Study_Q-Y4H0/bagit.txt'))
assert os.path.exists(os.path.join(test_output_path, 'Study_Q-Y4H0/data/assets/Study/Q-Y4H0/Experiment/Q-Y4BY/Replicate/Q-Y5F8/hMARIS_SIX2+_RiboDep#1.gene.rpkm.txt'))
\ No newline at end of file
workflow/tests/test_inferMetadata.py 0 → 100644
+ 14
− 0
View file @ 03aa79a9
#!/usr/bin/env python3
import pytest
import pandas as pd
from io import StringIO
import os
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
@pytest.mark.inferMetadata
def test_inferMetadata():
assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.se.sorted.deduped.tin.xls'))
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