Commit 6a95d28f authored by fmortreu's avatar fmortreu
Browse files

RNAseq_add_kallisto

parent 2fa2ee10
log.info "fastq files : ${params.fastq}"
log.info "fasta file : ${params.fasta}"
log.info "bed file : ${params.bed}"
log.info "fasta files : ${params.fasta}"
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
params.fasta = "$baseDir/data/bam/*.fasta"
params.fasta = "$baseDir/data/fasta/*.fasta"
params.bed = "$baseDir/data/annot/*.bed"
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
params.index = "$baseDir/data/index/*.index.*"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
params.fasta = "$baseDir/data/fasta/*.fasta"
params.bed = "$baseDir/data/annot/*.bed"
Channel
.fromPath( params.index )
.ifEmpty { error "Cannot find any index files matching: ${params.index}" }
.set { index_files }
Channel
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
.set { fasta_file }
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.set { fasta_files }
Channel
Channel
.fromPath( params.bed )
.ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
.set { bed_files }
......@@ -73,3 +92,41 @@ 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_file
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
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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