RNAseq : trim 60nt in 3' in cutadapt

src/RNAseq.config

@@ -8,8 +8,8 @@ profiles {
         container = "lbmc/fastqc:0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
-        cpus = 4
-        penv = 'openmp4'
+        cpus = 8
+        penv = 'openmp8'
         memory = "20GB"
         time = "12h"
         queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
@@ -27,8 +27,8 @@ profiles {
           container = "lbmc/fastqc:0.11.5"
           executor = "sge"
           clusterOptions = "-cwd -V"
-          cpus = 4
-          penv = 'openmp4'
+          cpus = 8
+          penv = 'openmp8'
           memory = "20GB"
           time = "12h"
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
@@ -45,8 +45,8 @@ profiles {
           container = "lbmc/fastqc:0.11.5"
           executor = "sge"
           clusterOptions = "-cwd -V"
-          cpus = 4
-          penv = 'openmp4'
+          cpus = 8
+          penv = 'openmp8'
           memory = "20GB"
           time = "12h"
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
@@ -85,8 +85,8 @@ profiles {
           container = "lbmc/fastqc:0.11.5"
           executor = "sge"
           clusterOptions = "-cwd -V"
-          cpus = 4
-          penv = 'openmp4'
+          cpus = 8
+          penv = 'openmp8'
           memory = "20GB"
           time = "12h"
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
@@ -161,8 +161,8 @@ profiles {
           container = "lbmc/fastqc:0.11.5"
           executor = "sge"
           clusterOptions = "-cwd -V"
-          cpus = 4
-          penv = 'openmp4'
+          cpus = 8
+          penv = 'openmp8'
           memory = "20GB"
           time = "12h"
           queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'

src/RNAseq.nf

@@ -133,7 +133,7 @@ process trimming {
   output:
   set file_id, "*cut_{R1,R2}.fastq.gz" into CUTADAPT_OUTPUT
   file "*first_report.txt" into CUTADAPT_LOG
-  file "*{second,third}_report.txt" into CUTADAPT_LOG_2
+//  file "*{second,third}_report.txt" into CUTADAPT_LOG_2
 
 
   script:
@@ -141,22 +141,32 @@ process trimming {
   cutadapt -j ${task.cpus} \
            -a ${params.adaptorR1} \
            -A ${params.adaptorR2} \
-           -o ${file_id}_tmp_R1.fastq.gz \
-           -p ${file_id}_tmp_R2.fastq.gz \
-           --minimum-length 70 \
-           ${reads[0]} ${reads[1]} > ${file_id}_first_report.txt
-
-  cutadapt -j ${task.cpus} \
-           -a "A{100}" \
+           -u -60 \
+           -U -60 \
            -o ${file_id}_cut_R1.fastq.gz \
-           ${file_id}_tmp_R1.fastq.gz \
-              > ${file_id}_second_report.txt
+           -p ${file_id}_cut_R2.fastq.gz \
+           --minimum-length 50 \
+           ${reads[0]} ${reads[1]} > ${file_id}_first_report.txt
 
-  cutadapt -j ${task.cpus} \
-         -u -60 \
-         -o ${file_id}_cut_R2.fastq.gz \
-         ${file_id}_tmp_R2.fastq.gz \
-           > ${file_id}_third_report.txt
+#  cutadapt -j ${task.cpus} \
+#           -a ${params.adaptorR1} \
+#           -A ${params.adaptorR2} \
+#           -o ${file_id}_tmp_R1.fastq.gz \
+#           -p ${file_id}_tmp_R2.fastq.gz \
+#           --minimum-length 70 \
+#           ${reads[0]} ${reads[1]} > ${file_id}_first_report.txt
+
+#  cutadapt -j ${task.cpus} \
+#           -a "A{100}" \
+#           -o ${file_id}_cut_R1.fastq.gz \
+#           ${file_id}_tmp_R1.fastq.gz \
+#              > ${file_id}_second_report.txt
+
+#  cutadapt -j ${task.cpus} \
+#         -u -60 \
+#         -o ${file_id}_cut_R2.fastq.gz \
+#         ${file_id}_tmp_R2.fastq.gz \
+#           > ${file_id}_third_report.txt
   """
 }
 
@@ -486,8 +496,8 @@ hisat2 -x ${index2_id} \
        --trim5 1\
        2> ${file_id}_postgenome.txt \
 | samtools view -bS -F 4 - \
-| samtools sort -@ ${task.cpus} -o ${file_id}.bam \
-&& samtools index ${file_id}.bam
+| samtools sort -@ ${task.cpus} -o ${file_id}_postgenome.bam \
+&& samtools index ${file_id}_postgenome.bam
 
 if grep -q "ERR" ${file_id}_postgenome.txt; then
   exit 1