From e2c3dace3913bf1fd2152d1e626a0b5a30b493e6 Mon Sep 17 00:00:00 2001 From: mherbett <marion.herbette@ens-lyon.fr> Date: Wed, 6 Jun 2018 15:01:22 +0000 Subject: [PATCH] RNAseq.n : add kallisto block fo paid nd --- src/RNASeq.nf | 76 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) diff --git a/src/RNASeq.nf b/src/RNASeq.nf index 86afe64..9dd795f 100644 --- a/src/RNASeq.nf +++ b/src/RNASeq.nf @@ -111,3 +111,79 @@ bedtools getfasta -name \ """ } +/* +* Kallisto : +* Imputs : fastq files +* Imputs : fasta files +* Output : bam files +*/ + +/* fasta indexing */ +params.fasta = "$baseDir/data/bam/*.fasta" + +log.info "fasta files : ${params.fasta}" + +Channel + .fromPath( params.fasta ) + .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" } + .set { fasta_file } + +process index_fasta { + tag "$fasta.baseName" + publishDir "results/mapping/index/", mode: 'copy' + + input: + file fasta from fasta_file + + output: + file "*.index*" into index_files + + script: +""" +kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \ +> ${fasta.baseName}_kallisto_report.txt +""" +} + + +/* +* for paired-end data +*/ + +params.fastq = "$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: ${params.index}" } + .set { index_files } + +process mapping_fastq { + tag "$reads" + cpus 4 + publishDir "results/mapping/quantification/", mode: 'copy' + + input: + file reads from fastq_files + 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 +""" +} + + -- GitLab