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RNA_Seq.nf 3.28 KiB
/*
* cutadapt :
* Imputs : fastq files
* Output : fastq files
*/
/* Illumina adaptor removal */
/*
* for paired-end data
*/
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
log.info "fastq files : ${params.fastq}"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process adaptor_removal {
tag "$pair_id"
publishDir "results/fastq/adaptor_removal/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
output:
file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
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]} > ${pair_id}_report.txt
"""
}
/*
* urqt :
* Imputs : fastq files
* Output : fastq files
*/
/* quality trimming */
/*
* for paired-end data
*/
process trimming {
tag "${reads}"
cpus 4
publishDir "results/fastq/trimming/", mode: 'copy'
input:
file reads from fastq_files_cut
output:
file "*_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 ${reads[0].baseName}_trim_R1.fastq.gz --outpair ${reads[1].baseName}_trim_R2.fastq.gz \
> ${reads[0].baseName}_trimming_report.txt
"""
}
/*
* bedtools :
* Imputs : fastq files
* Output : fastq files
*/
/* fasta extraction */
params.fasta = "$baseDir/data/fasta/*.fasta"
params.bed = "$baseDir/data/annot/*.bed"
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: ${params.bed}" }
.set { bed_files }
process fasta_from_bed {
tag "${bed.baseName}"
cpus 4
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 ${bed.baseName}_extracted.fasta
"""
}
/*
* Kallisto :
* Imputs : fastq files
* Imputs : fasta files
* Output : bam files
*/
/* fasta indexing */
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
input:
file fasta from fasta_files
output:
file "*.index*" into index_files
script:
"""
kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
> ${fasta.baseName}_kallisto_report.txt
"""
}
/*
* for paired-end data
*/
process mapping_fastq {
tag "$reads"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
input:
file reads from fastq_files_trim
file index from index_files.toList()
output:
file "*" into counts_files
script:
"""
mkdir ${reads[0].baseName}
kallisto quant -i ${index} -t ${task.cpus} \
--bias --bootstrap-samples 100 -o ${reads[0].baseName} \
${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
"""
}