fix beugs in RNAseq pipeline

src/RNAseq.config

@@ -3,7 +3,7 @@ profiles {
     process{
       withName: trimming {
         beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/cutadapt_2.1"
+        conda = "$baseDir/.conda_envs/cutadapt_2.4"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/RNAseq.nf

@@ -27,11 +27,11 @@ process trimming {
   script:
   """
   cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC \
-  -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_tmp_R2.fastq.gz \
-  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+  -o ${file_id}_cut_R1.fastq.gz -p ${file_id}_tmp_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${file_id}_report.txt
 
-  cutadapt -u -14 -o ${pair_id}_cut_R2.fastq.gz ${pair_id}_tmp_R2.fastq.gz \
-  > ${pair_id}_cut_report.txt
+  cutadapt -u -14 -o ${file_id}_cut_R2.fastq.gz ${file_id}_tmp_R2.fastq.gz \
+  > ${file_id}_cut_report.txt
   """
 }
 
@@ -82,13 +82,13 @@ log.info "index : ${params.index_hg38}"
 Channel
   .fromPath ( params.index_hg38 )
   .ifEmpty { error "Cannot find any hg38 index files matching: ${params.index_hg38}" }
-  .set { index_file_hg38 }--paired
+  .set { index_file_hg38 }
 
 process hisat2_human {
   tag "$file_id"
 
   input:
-    set file_id, file(fastq_filtred) from rRNA_removed_reads
+    set file_id, file(fastq_filtred) from rRNA_removed_files
     file index from index_file_hg38.toList()
 
   output: