src/RibosomeProfiling.nf : trim 1 base at 5' and 3' end by hisat

src/RibosomeProfiling.nf

@@ -276,6 +276,9 @@ hisat2 -x ${index_id} \
        --un-gz ${file_id}_notaligned.fastq.gz \
        --rna-strandness ${params.strand} \
        --dta \
+       --no-softclip \
+       --trim5 1\
+       --trim3 1\
        2> ${file_id}_genome.txt \
 | samtools view -bS -F 4 - \
 | samtools sort -@ ${task.cpus} -o ${file_id}.bam \
@@ -316,29 +319,29 @@ process fastqc_genome {
 /* Deduplication of reads */
 ////////////////////////////
 
-process dedup_genome {
-  tag "$file_id"
-  publishDir "${params.output}/03_hisat2/dedup/", mode: 'copy'
+if (params.do_dedup) {
+  process dedup_genome {
+    tag "$file_id"
+    publishDir "${params.output}/03_hisat2/dedup/", mode: 'copy'
 
-  input:
-  set file_id, file(bam) from HISAT_ALIGNED_DEDUP
+    input:
+    set file_id, file(bam) from HISAT_ALIGNED_DEDUP
 
-  output:
-  set file_id, "*.{bam, bai}" into DEDUP_GENOME
-  file "*.log" into DEDUP_LOG
+    output:
+    set file_id, "*.{bam, bai}" into DEDUP_GENOME
+    file "*.log" into DEDUP_LOG
 
-  when:
-  params.do_dedup
+    when:
+    params.do_dedup
 
-    """
-    umi_tools dedup -I ${bam[0]} \
-    -S ${file_id}.dedup.bam \
-    > ${file_id}_dedup.log
-    """
-}
-
-if (! params.do_dedup) {
-  HISAT_ALIGNED_DEDUP.into{DEDUP_GENOME}
+      """
+      umi_tools dedup -I ${bam[0]} \
+      -S ${file_id}.dedup.bam \
+      > ${file_id}_dedup.log
+      """
+  }
+} else {
+  HISAT_ALIGNED_DEDUP.set{DEDUP_GENOME}
 }
 
 DEDUP_GENOME.into{DEDUP_GENOME_HTSEQ;
@@ -456,7 +459,7 @@ hisat2 -x ${index2_id} \
        --rna-strandness ${params.strand} \
        --dta\
        2> ${file_id}_postgenome.txt \
-| samtools view -bS -F 4 - \
+| samtools view -bS -F 4 -F 256 - \
 | samtools sort -@ ${task.cpus} -o ${file_id}.bam \
 && samtools index ${file_id}.bam
 
@@ -473,25 +476,29 @@ POSTGENOME_ALIGNED.into{POSTGENOME_ALIGNED_FASTQC;
 /* Deduplication of reads */
 ////////////////////////////
 
-process dedup_postgenome {
-  tag "$file_id"
-  publishDir "${params.output}/05_post_genome_hisat2/dedup/", mode: 'copy'
+if (params.do_dedup){
+  process dedup_postgenome {
+    tag "$file_id"
+    publishDir "${params.output}/05_post_genome_hisat2/dedup/", mode: 'copy'
 
-  input:
-  set file_id, file(bam) from POSTGENOME_ALIGNED_DEDUP
+    input:
+    set file_id, file(bam) from POSTGENOME_ALIGNED_DEDUP
 
-  output:
-  set file_id, "*.{bam, bai}" into DEDUP_POSTGENOME
-  file "*.log" into DEDUP_POSTGENOME_LOG
+    output:
+    set file_id, "*.{bam, bai}" into DEDUP_POSTGENOME
+    file "*.log" into DEDUP_POSTGENOME_LOG
 
-  when:
-  params.do_dedup
+    when:
+    params.do_dedup
+
+    """
+    umi_tools dedup -I ${bam[0]} \
+    -S ${file_id}.dedup.bam \
+    > ${file_id}_dedup.log
+    """
+  }
+} else {
 
-  """
-  umi_tools dedup -I ${bam[0]} \
-  -S ${file_id}.dedup.bam \
-  > ${file_id}_dedup.log
-  """
 }
 
 process fastqc_postgenome {