Unverified Commit a2f9dcc6 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

Merge branch 'Delattre/JU28_59vs17_SNP-master' into dev to get BWA GATK...

Merge branch 'Delattre/JU28_59vs17_SNP-master' into dev to get BWA GATK sambamba samblaster and bcftools
parents aac64942 3ecf28b8
......@@ -2,3 +2,4 @@ nextflow
.nextflow.log*
.nextflow/
work/
results
FROM sambamba:0.6.7
MAINTAINER Laurent Modolo
ENV BWA_VERSION=0.7.17
ENV SAMBLASTER_VERSION=0.1.24
ENV PACKAGES curl=7.58.0* \
ca-certificates=20180409 \
build-essential=12.4* \
zlib1g-dev=1:1.2.11*
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
RUN curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
cd bwa-${BWA_VERSION}/ && \
make && \
cp bwa /usr/bin && \
cd .. && \
rm -R bwa-${BWA_VERSION}/
RUN curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
cd samblaster-v.${SAMBLASTER_VERSION}/ && \
make && \
cp samblaster /usr/bin && \
cd .. && \
rm -R samblaster-v.${SAMBLASTER_VERSION}/
#!/bin/sh
docker build src/docker_modules/BWA/0.7.17 -t 'bwa:0.7.17'
FROM broadinstitute/gatk:4.0.8.1
MAINTAINER Laurent Modolo
ENV GATK_VERSION=4.0.8.1
RUN cp gatk /usr/bin/
#!/bin/sh
docker build src/docker_modules/GATK/4.0.8.1 -t 'gatk:4.0.8.1'
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
ENV BCFTOOLS_VERSION=1.7
ENV PACKAGES bcftools=${BCFTOOLS_VERSION}*
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
#!/bin/sh
docker build src/docker_modules/bcftools/1.7 -t 'bcftools:1.7'
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
ENV BIOAWK_VERSION=1.0
ENV PACKAGES git=1:2.17* \
build-essential=12.4* \
ca-certificates=20180409 \
zlib1g-dev=1:1.2.11* \
byacc
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
RUN git clone https://github.com/lh3/bioawk.git && \
cd bioawk && \
git checkout tags/v${BIOAWK_VERSION} && \
make && \
cd .. && \
mv bioawk/bioawk /usr/bin/ && \
rm -Rf bioawk
#!/bin/sh
docker build src/docker_modules/bioawk/1.0 -t 'bioawk:1.0'
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
ENV SAMBAMBA_VERSION=0.6.7
ENV PACKAGES curl=7.58.0* \
ca-certificates=20180409 \
build-essential=12.4* \
zlib1g-dev=1:1.2.11*
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
RUN curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
mv sambamba /usr/bin/ && \
rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
#!/bin/sh
docker build src/docker_modules/sambamba/0.6.7 -t 'sambamba:0.6.7'
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
ENV SAMBLASTER_VERSION=0.1.24
ENV PACKAGES curl=7.58.0* \
ca-certificates=20180409 \
build-essential=12.4* \
zlib1g-dev=1:1.2.11*
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
RUN curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
cd samblaster-v.${SAMBLASTER_VERSION}/ && \
make && \
cp samblaster /usr/bin && \
cd .. && \
rm -R samblaster-v.${SAMBLASTER_VERSION}/
#!/bin/sh
docker build src/docker_modules/samblaster/0.1.24 -t 'samblaster:0.1.24'
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$index_fasta {
container = "bwa:0.7.17"
}
}
}
sge {
process{
$index_fasta {
beforeScript = "module purge; module load BWA/0.7.17"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
}
}
}
params.fasta = "$baseDir/data/bam/*.fasta"
log.info "fasta files : ${params.fasta}"
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fasta_file }
process index_fasta {
tag "$fasta_id"
cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
set fasta_id, file(fasta) from fasta_file
output:
set fasta_id, "${fasta.baseName}.*" into index_files
file "*_bwa_report.txt" into index_files_report
script:
"""
bwa index -p ${fasta.baseName} ${fasta} \
&> ${fasta.baseName}_bwa_report.txt
"""
}
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$mapping_fastq {
container = "bwa:0.7.17"
}
}
}
sge {
process{
$mapping_fastq {
beforeScript = "module purge; module load BWA/0.7.17"
executor = "sge"
cpus = 4
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
}
}
}
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
params.index = "$baseDir/data/index/*.index.*"
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
Channel
.fromPath( params.index )
.ifEmpty { error "Cannot find any index files matching: ${params.index}" }
.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.groupTuple()
.set { index_files }
process mapping_fastq {
tag "$reads"
cpus 4
publishDir "results/mapping/sam/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
set index_id, file(index) from index_files.collect()
output:
file "${pair_id}.sam" into sam_files
file "${pair_id}_bwa_report.txt" into mapping_repport_files
script:
"""
bwa mem -t ${task.cpus} \
${index_id} ${reads[0]} ${reads[1]} \
-o ${pair_id}.sam &> ${pair_id}_bwa_report.txt
"""
}
./nextflow src/nf_modules/BWA/indexing.nf \
-c src/nf_modules/BWA/indexing.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
# ./nextflow src/nf_modules/BWA/mapping_single.nf \
# -c src/nf_modules/BWA/mapping_single.config \
# -profile docker \
# --index "results/mapping/index/tiny_v2.index" \
# --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
./nextflow src/nf_modules/BWA/mapping_paired.nf \
-c src/nf_modules/BWA/mapping_paired.config \
-profile docker \
--index "results/mapping/index/tiny_v2*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$index_bam {
container = "sambamba:0.6.7"
}
}
}
sge {
process{
$index_bam {
beforeScript = "module purge; module load sambamba/0.6.7"
}
}
}
}
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment