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Commit 00144f10 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Merge branch '8-makeBigWig' into 'develop' 

Resolve "process_makeBigWig"

Closes #8

See merge request !19
parents eac0a7c5 c1d6c6f6
2 merge requests!37v0.0.1,!19Resolve "process_makeBigWig"
Pipeline #6041 passed with stages
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.gitlab-ci.yml
+ 11
− 3
View file @ 00144f10
......@@ -51,11 +51,11 @@ 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/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
- 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/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' 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 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
......@@ -64,8 +64,16 @@ alignData:
dedupData:
stage: unit
script:
- singularity exec 'docker://bicf/picard2.21.7:2.0.0' 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' 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
- pytest -m dedupData
makeBigWig:
stage: unit
script:
- singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -p `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -o Q-Y5JA_1M.se.bw
- pytest -m makeBigWig
fastqc:
stage: unit
......
workflow/conf/biohpc.config
+ 3
− 0
View file @ 00144f10
......@@ -27,6 +27,9 @@ process {
withName: fastqc {
queue = 'super'
}
withName: makeBigWig {
queue = 'super'
}
}
singularity {
......
workflow/nextflow.config
+ 5
− 2
View file @ 00144f10
......@@ -30,11 +30,14 @@ process {
container = 'bicf/gudmaprbkaligner:2.0.0'
}
withName: dedupData {
container = 'bicf/picard2.21.7:2.0.0'
container = 'bicf/gudmaprbkdedup:2.0.0'
}
withName: fastqc {
container = 'bicf/fastqc:2.0.0'
}
withName: makeBigWig {
container = 'bicf/deeptools3.3:2.0.0'
}
}
trace {
......@@ -64,4 +67,4 @@ manifest {
mainScript = 'rna-seq.nf'
version = 'v0.0.1_indev'
nextflowVersion = '>=19.09.0'
}
\ No newline at end of file
}
workflow/rna-seq.nf
+ 58
− 17
View file @ 00144f10
#!/usr/bin/env nextflow
// ######## #### ###### ########
// ## ## ## ## ## ##
// ## ## ## ## ##
// ######## ## ## ######
// ## ## ## ## ##
// ## ## ## ## ## ##
// ######## #### ###### ##
// Define input variables
params.deriva = "${baseDir}/../test_data/auth/credential.json"
params.bdbag = "${baseDir}/../test_data/auth/cookies.txt"
//params.repRID = "16-1ZX4"
params.repRID = "Q-Y5JA"
params.refVersion = "0.0.1"
params.refMuVersion = "38.P6"
params.refHuVersion = "38.p12"
params.refMoVersion = "38.p6.vM22"
params.refHuVersion = "38.p12.v31"
params.outDir = "${baseDir}/../output"
// Parse input variables
......@@ -18,15 +25,15 @@ bdbag = Channel
.fromPath(params.bdbag)
.ifEmpty { exit 1, "deriva cookie file for bdbag not found: ${params.bdbag}" }
repRID = params.repRID
refVersion = params.refVersion
refMuVersion = params.refMuVersion
refMoVersion = params.refMoVersion
refHuVersion = params.refHuVersion
outDir = params.outDir
logsDir = "${outDir}/Logs"
// Define fixed files
derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
referenceBase = "s3://bicf-references"
//referenceBase = "s3://bicf-references"
referenceBase = "/project/BICF/BICF_Core/shared/gudmap/references"
// Define script files
script_bdbagFetch = Channel.fromPath("${baseDir}/scripts/bdbagFetch.sh")
......@@ -186,9 +193,11 @@ stranded.into {
}
spike.into{
spike_getRef
spike_rseqc
}
species.into {
species_getRef
species_rseqc
}
/*
......@@ -199,10 +208,6 @@ process getRef {
publishDir "${logsDir}", mode: "copy", pattern: "*.getRef.err"
input:
val referenceBase
val refVersion
val refMuVersion
val refHuVersion
val spike_getRef
val species_getRef
......@@ -215,13 +220,13 @@ process getRef {
ulimit -a >>${repRID}.getRef.err
export https_proxy=\${http_proxy}
# retreive appropriate reference from S3 bucket
# run set the reference name
if [ "${species_getRef}" == "Mus musculus" ]
then
references=\$(echo ${referenceBase}/mouse/${refVersion}/GRCm${refMuVersion})
references=\$(echo ${referenceBase}/GRCm${refMoVersion})
elif [ '${species_getRef}' == "Homo sapiens" ]
then
references=\$(echo ${referenceBase}/human/${refVersion}/GRCh${refHuVersion})
references=\$(echo ${referenceBase}/GRCh${refHuVersion})
else
exit 1
fi
......@@ -232,7 +237,17 @@ process getRef {
then
reference=\$(echo \${references}/)
fi
aws s3 cp "\${references}" ./ --recursive >>${repRID}.getRef.err
# retreive appropriate reference appropriate location
if [ ${referenceBase} == "s3://bicf-references" ]
then
aws s3 cp "\${references}" /hisat2 ./ --recursive >>${repRID}.getRef.err
aws s3 cp "\${references}" /bed ./ --recursive >>${repRID}.getRef.err
elif [ ${referenceBase} == "/project/BICF/BICF_Core/shared/gudmap/references" ]
then
cp -R "\${references}"/hisat2 ./ >>${repRID}.getRef.err
cp -R "\${references}"/bed ./ >>${repRID}.getRef.err
fi
"""
}
......@@ -268,6 +283,11 @@ process trimData {
"""
}
reference.into {
reference_alignData
reference_rseqc
}
/*
* alignData: aligns the reads to a reference database
*/
......@@ -279,7 +299,7 @@ process alignData {
val endsManual_alignData
val stranded_alignData
path fastq from fastqs_trimmed
path reference
path reference_alignData
output:
path ("${repRID}.sorted.bam") into rawBam
......@@ -320,7 +340,7 @@ process dedupData {
path rawBam
output:
path ("${repRID}.deduped.bam") into dedupBam
tuple val ("${repRID}"), path ("${repRID}.sorted.deduped.bam"), path ("${repRID}.sorted.deduped.bai") into dedupBam
path ("${repRID}.dedup.out")
path ("${repRID}.dedup.err")
......@@ -331,6 +351,8 @@ process dedupData {
# 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
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>> ${repRID}.dedup.err
"""
}
......@@ -356,4 +378,23 @@ process fastqc {
# run fastqc
fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
"""
}
\ No newline at end of file
}
/*
*Make BigWig files for later processes
*/
process makeBigWig {
tag "${repRID}"
publishDir "${logsDir}", mode: 'copy', pattern: "*.makeBigWig.err"
input:
set val (repRID), path (inBam), path (inBai) from dedupBam
output:
path ("${repRID}.bw")
script:
"""
bamCoverage -p `nproc` -b ${inBam} -o ${repRID}.bw
"""
}
workflow/tests/test_makeBigWig.py 0 → 100644
+ 14
− 0
View file @ 00144f10
#!/usr/bin/env python3
import pytest
import pandas as pd
import os
import utils
data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
@pytest.mark.makeBigWig
def test_makeBigWig():
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.bw'))
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