hisat2: remove samtools report

src/nf_modules/hisat2/main.nf

@@ -77,10 +77,8 @@ process mapping_fastq {
     -1 ${reads[0]} \
     -2 ${reads[1]} 2> \
     ${file_prefix}_ht2_mapping_report.txt \
-    | samtools view -@ ${task.cpus} -bS - 2>> \
-    ${file_prefix}_ht2_samtools_view_report.txt \
-    | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
-    ${file_prefix}_ht2_samtools_sort_report.txt
+    | samtools view -@ ${task.cpus} -bS - \
+    | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam
 
   if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then
     exit 1
@@ -93,11 +91,8 @@ process mapping_fastq {
     -x ${index_id} \
     -U ${reads} 2> \
     ${file_prefix}_ht2_mapping_report.txt \
-    | samtools view -@ ${task.cpus} -bS - 2>> \
-    ${file_prefix}_ht2_samtools_view_report.txt \
-    | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
-    ${file_prefix}_ht2_samtools_sort_report.txt
-
+    | samtools view -@ ${task.cpus} -bS - \
+    | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam
   if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then
     exit 1
   fi