Update main.nf

main.nf

@@ -813,28 +813,28 @@ if(params.aligner == 'hisat2' && !params.skip_alignment){
  }
 }
 
-process sort_by_name_BAM {
- tag "${bam_featurecounts.baseName - '.sorted'}"
+if(!params.skip_alignment){
+ process sort_by_name_BAM {
+ tag "${bam_featurecounts.baseName - '.sorted'}"
 
- when:
- !params.skip_alignment
-
- input:
- file bam_featurecounts
+ input:
+ file bam_featurecounts
 
- output:
- file "${bam_featurecounts.baseName}ByName.bam" into bam_featurecounts_sorted, bam_count_exons
+  output:
+  file "${bam_featurecounts.baseName}ByName.bam" into bam_featurecounts_sorted, bam_count_exons
 
- script:
- def avail_mem = task.memory ? "-m ${task.memory.toBytes() / (task.cpus + 2)}" : ''
- """
- samtools sort -n \\
- $bam_featurecounts \\
- -@ ${task.cpus} $avail_mem \\
- -o ${bam_featurecounts.baseName}ByName.bam
- """
+ script:
+ def avail_mem = task.memory ? "-m ${task.memory.toBytes() / (task.cpus + 2)}" : ''
+ """
+ samtools sort -n \\
+ $bam_featurecounts \\
+ -@ ${task.cpus} $avail_mem \\
+ -o ${bam_featurecounts.baseName}ByName.bam
+ """
+ }
 }
 
+
 /*
  * STEP 3Salmon.1 - quant transcripts with Salmon
  */