RNAseq.nf : update

src/RNAseq.nf

@@ -11,9 +11,22 @@
 */
 
 params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+params.fasta = "$baseDir/data/fasta/*.fasta"
+params.bed = "$baseDir/data/annot/*.bed"
 
 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
   .fromFilePairs( params.fastq )
   .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
@@ -75,20 +88,11 @@ UrQt --t 20 --m ${task.cpus} --gz \
 */
 /*                      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}"
@@ -118,14 +122,6 @@ bedtools getfasta -name \
 */
 
 /*                      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"
@@ -149,20 +145,6 @@ kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
 * 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"
@@ -190,24 +172,6 @@ ${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
 * for single-end data
 */
 
-params.fastq = "$baseDir/data/fastq/*.fastq"
-params.index = "$baseDir/data/index/*.index*"
-params.mean = 200
-params.sd = 100
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-log.info "mean read size: ${params.mean}"
-log.info "sd read size: ${params.sd}"
-
-Channel
-  .fromPath( 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.baseName"
@@ -215,8 +179,8 @@ process mapping_fastq {
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:
-  file reads from fastq_files
-  file index from index_files.toList()
+  file reads from fastq_files_trim
+  file index from index_files
 
   output:
   file "*" into count_files