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 \
@@ -316,6 +319,7 @@ process fastqc_genome {
 /* Deduplication of reads */
 ////////////////////////////
 
+if (params.do_dedup) {
   process dedup_genome {
     tag "$file_id"
     publishDir "${params.output}/03_hisat2/dedup/", mode: 'copy'
@@ -336,9 +340,8 @@ process dedup_genome {
       > ${file_id}_dedup.log
       """
   }
-
-if (! params.do_dedup) {
-  HISAT_ALIGNED_DEDUP.into{DEDUP_GENOME}
+} 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
 
@@ -473,6 +476,7 @@ POSTGENOME_ALIGNED.into{POSTGENOME_ALIGNED_FASTQC;
 /* Deduplication of reads */
 ////////////////////////////
 
+if (params.do_dedup){
   process dedup_postgenome {
     tag "$file_id"
     publishDir "${params.output}/05_post_genome_hisat2/dedup/", mode: 'copy'
@@ -493,6 +497,9 @@ process dedup_postgenome {
     > ${file_id}_dedup.log
     """
   }
+} else {
+
+}
 
 process fastqc_postgenome {
   tag "$file_id"