RNAseq_add_kallisto

src/RNAseq.nf

 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
+"""
+}