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Unverified Commit 0a015caa authored by Laurent Modolo's avatar Laurent Modolo
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RNASeq: add experimental biologists practical solution

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src/RNASeq.config
+ 122
− 4
View file @ 0a015caa
...@@ -4,9 +4,25 @@ profiles { ...@@ -4,9 +4,25 @@ profiles {
docker.enabled = true docker.enabled = true
process { process {
withName: adaptor_removal { withName: adaptor_removal {
container = "lbmc/cutadapt:2.4" container = "lbmc/cutadapt:2.1"
cpus = 1 cpus = 1
} }
withName: trimming {
cpus = 4
container = "lbmc/urqt:d62c1f8"
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: index_fasta {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
} }
} }
singularity { singularity {
...@@ -14,16 +30,53 @@ profiles { ...@@ -14,16 +30,53 @@ profiles {
singularity.cacheDir = "./bin/" singularity.cacheDir = "./bin/"
process { process {
withName: adaptor_removal { withName: adaptor_removal {
container = "lbmc/cutadapt:2.4" container = "lbmc/cutadapt:2.1"
cpus = 1
}
withName: trimming {
cpus = 4
container = "lbmc/urqt:d62c1f8"
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
cpus = 1 cpus = 1
} }
withName: index_fasta {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
} }
} }
psmn{ psmn{
process{ process{
withName: adaptor_removal { withName: adaptor_removal {
beforeScript = "source $baseDir/.conda_psmn.sh" beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.4" conda = "$baseDir/.conda_envs/cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
withName: trimming {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/urqt_d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "5GB"
cpus = 16
time = "12h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
}
withName: fasta_from_bed {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bedtools_2.25.0"
executor = "sge" executor = "sge"
clusterOptions = "-cwd -V" clusterOptions = "-cwd -V"
cpus = 1 cpus = 1
...@@ -31,6 +84,28 @@ profiles { ...@@ -31,6 +84,28 @@ profiles {
time = "12h" time = "12h"
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
} }
withName: index_fasta {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
}
withName: mapping_fastq {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
}
} }
} }
ccin2p3 { ccin2p3 {
...@@ -39,7 +114,28 @@ profiles { ...@@ -39,7 +114,28 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch" singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{ process{
withName: adaptor_removal { withName: adaptor_removal {
container = "lbmc/cutadapt:2.4" container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
withName: trimming {
container = "lbmc/urqt:d62c1f8"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
scratch = true scratch = true
stageInMode = "copy" stageInMode = "copy"
stageOutMode = "rsync" stageOutMode = "rsync"
...@@ -48,6 +144,28 @@ profiles { ...@@ -48,6 +144,28 @@ profiles {
cpus = 1 cpus = 1
queue = 'huge' queue = 'huge'
} }
withName: index_fasta {
container = "lbmc/kallisto:0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
} }
} }
} }
src/RNASeq.nf
+ 91
− 4
View file @ 0a015caa
log.info "fastq files : ${params.fastq}" log.info "fastq files : ${params.fastq}"
log.info "fasta file : ${params.fasta}"
log.info "bed file : ${params.bed}"
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.set { fasta_files }
Channel
.fromPath( params.bed )
.ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
.set { bed_files }
Channel Channel
.fromFilePairs( params.fastq ) .fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" } .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
...@@ -16,9 +26,86 @@ process adaptor_removal { ...@@ -16,9 +26,86 @@ process adaptor_removal {
set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
script: script:
"""
cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
-o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
""" """
cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
-o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
process trimming {
tag "${reads}"
publishDir "results/fastq/trimming/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files_cut
output:
set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
script:
"""
UrQt --t 20 --m ${task.cpus} --gz \
--in ${reads[0]} --inpair ${reads[1]} \
--out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
> ${pair_id}_trimming_report.txt
"""
}
process fasta_from_bed {
tag "${bed.baseName}"
publishDir "results/fasta/", mode: 'copy'
input:
file fasta from fasta_files
file bed from bed_files
output:
file "*_extracted.fasta" into fasta_files_extracted
script:
"""
bedtools getfasta -name \
-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
"""
}
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
input:
file fasta from fasta_files_extracted
output:
file "*.index*" into index_files
file "*_kallisto_report.txt" into index_files_report
script:
"""
kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
2> ${fasta.baseName}_kallisto_report.txt
"""
}
process mapping_fastq {
tag "$reads"
publishDir "results/mapping/quantification/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files_trim
file index from index_files.collect()
output:
file "*" into counts_files
script:
"""
mkdir ${pair_id}
kallisto quant -i ${index} -t ${task.cpus} \
--bias --bootstrap-samples 100 -o ${pair_id} \
${reads[0]} ${reads[1]} &> ${pair_id}/kallisto_report.txt
"""
} }
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