Apply suggestions from code review

Co-authored-by: Harshil Patel <[email protected]>

Author: pinin4fjords

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v3.14.0 - 2024-01-05
+## v3.14.0 - 2024-01-08
 
 ### Credits
 

conf/modules.config

@@ -377,7 +377,6 @@ if (!params.skip_alignment) {
                 path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
                         ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
                     ) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
-                path: { "${params.outdir}/${params.aligner}" },
                 mode: params.publish_dir_mode,
                 pattern: "*.{bai,csi}",
                 saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
@@ -662,7 +661,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
             withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
                 ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
                 publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}/samtools_stats" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.{stats,flagstat,idxstats}',
                     saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }

workflows/rnaseq.nf

@@ -364,7 +364,9 @@ workflow RNASEQ {
         .set { ch_strand_fastq }
 
     // Return empty channel if ch_strand_fastq.auto_strand is empty so salmon index isn't created
-    PREPARE_GENOME.out.fasta
+    PREPARE_GENOME
+        .out
+        .fasta
         .combine(ch_strand_fastq.auto_strand)
         .map { it.first() }
         .first()