fix beug in RNAseq pipeline

src/RNAseq.config

@@ -41,16 +41,6 @@ profiles {
         time = "12h"
         queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
-      withName: index_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/hisat2_2.1.0"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
-      }
       withName: counting {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "htseq/0.11.2"
@@ -83,14 +73,6 @@ profiles {
         container = "lbmc/samtools:1.7"
         cpus = 1
       }
-      withName: index_bam {
-        container = "lbmc/samtools:1.7"
-        cpus = 1
-      }
-      withName: dedup {
-        container = "lbmc/umi_tools:1.0.0"
-        cpus = 1
-      }
       withName: counting {
         container = "lbmc/htseq:0.11.2"
         cpus = 1

src/RNAseq.nf

@@ -94,14 +94,16 @@ Channel
 
 process hisat2_human {
   tag "$file_id"
+  publishDir "${params.output}/03_hisat2/", mode: 'copy'
+  errorStrategy 'finish'
 
   input:
     set file_id, file(fastq_filtred) from rRNA_removed_files
     file index from index_file_hg38.toList()
 
   output:
-    set file_id, "*.fastq.gz" into reads_non_aligned_hg38
-    set file_id, "*.bam" into reads_aligned_hg38
+    file "*.fastq.gz" into reads_non_aligned_hg38
+    set file_id, "*_sorted.{bam,bam.bai}" into sorted_bam_files
     file "*.txt" into hisat_report
 
   script:
@@ -115,51 +117,33 @@ process hisat2_human {
 hisat2 -x ${index_id} -p ${task.cpus} \
 -1 ${fastq_filtred[0]} -2 ${fastq_filtred[1]} \
 --un-conc-gz ${file_id}_notaligned_R%.fastq.gz \
---rna-strandness 'F' \
-2> ${file_id}_hisat2_hg38.txt | samtools view -bS -F 4 -o ${file_id}.bam
-
-"""
-}
-
-reads_aligned_hg38.into{for_mapping;for_htseq}
-
-
-/*                   sorting                             */
-
-process index_bam {
-  tag "$file_id"
-  publishDir "${params.output}/03_hisat2/", mode: 'copy'
+--rna-strandness 'F' 2> ${file_id}_hisat2_hg38.txt | samtools view -bS -F 4 -o ${file_id}.bam
 
-  input:
-    set file_id, file(bam) from for_mapping
-    file report from hisat_report
-
-  output:
-    set file_id, "*_sorted.{bam,bam.bai}" into sorted_bam_files
-    file "*.txt" into report_hisat
+if grep -q "ERR" ${file_id}_hisat2_hg38.txt; then
+  exit 1
+fi
 
-  script:
-"""
-samtools sort -@ ${task.cpus} -O BAM -o ${file_id}_sorted.bam ${bam}
+samtools sort -@ ${task.cpus} -O BAM -o ${file_id}_sorted.bam ${file_id}.bam
 samtools index ${file_id}_sorted.bam
-cat ${report} > ${file_id}_hisat_hg38.txt
+
 """
 }
 
+
 /*                   HTseq                            */
 
 process sort_bam {
   tag "$file_id"
 
   input:
-    set file_id, file(bam) from for_htseq
+    set file_id, file(bam) from sorted_bam_files
 
   output:
-    set file_id, "*_sorted.bam" into sorted_bam_files_2
+    set file_id, "*_htseq.bam" into sorted_bam_files_2
 
   script:
 """
-samtools sort -@ ${task.cpus} -n -O BAM -o ${file_id}_sorted.bam ${bam}
+samtools sort -@ ${task.cpus} -n -O BAM -o ${file_id}_htseq.bam ${bam[0]}
 """
 }
 

src/dual_mapping_paired.nf

@@ -4,6 +4,8 @@
 
 params.fasta = "data/genome/NC001802.1.fa"
 log.info "fasta files : ${params.fasta}"
+params.output = "results"
+log.info "saving file into ${params.output}"
 
 Channel
   .fromPath( params.fasta )
@@ -122,15 +124,15 @@ for (index_file in index) {
   }
 }
 """
-bowtie2 --best --fr -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+bowtie2 --sensitive --fr -p ${task.cpus} -x ${index_id} \
 -1 ${reads[0]} -2 ${reads[1]} 2> \
 ${file_id}_bowtie2_report_tmp.txt | \
 samtools view -F 4 -F 16 -Sb - > ${file_id}_bowtie.bam
 
-if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
+if grep -q "Error" ${file_id}_bowtie2_report_tmp.txt; then
   exit 1
 fi
-tail -n 19 ${file_id}_bowtie_report_tmp.txt > ${file_id}_bowtie_report.txt
+tail -n 19 ${file_id}_bowtie2_report_tmp.txt > ${file_id}_bowtie2_report.txt
 """
 }
 
@@ -144,7 +146,7 @@ bam_bowtie.join(bam_hisat)
 //merged_bam.println()
 
 process merge_bam{
-  publishDir "results/05_${index_id}_mergedBAM/", mode: 'copy'
+  publishDir "${params.output}/05_${index_id}_mergedBAM/", mode: 'copy'
 
   input:
   set file_id, index_id, file(bam_bowtie), file(bam_hisat) from merged_bam