From cc63dff641d04da8c0fff0cea31d903a918de2b3 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Thu, 4 Jan 2024 12:01:45 +0000
Subject: [PATCH 1/6] Disable additional multiqc versions section

---
 assets/multiqc_config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 16bf186b3..3dfec8dcb 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -9,6 +9,7 @@ report_section_order:
     order: -1002
 
 export_plots: true
+disable_version_detection: true
 
 # Run only these modules
 run_modules:

From e86ea029b8e34e0e9a50fb7e90024ac14e147719 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Thu, 4 Jan 2024 14:58:35 +0000
Subject: [PATCH 2/6] Defer strand inference until after trimming and filtering

---
 workflows/rnaseq.nf | 95 +++++++++++++++++++++++----------------------
 1 file changed, 48 insertions(+), 47 deletions(-)

diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
index f8def2d10..178d9003a 100755
--- a/workflows/rnaseq.nf
+++ b/workflows/rnaseq.nf
@@ -244,47 +244,6 @@ workflow RNASEQ {
     .set { ch_cat_fastq }
     ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null))
 
-    // Branch FastQ channels if 'auto' specified to infer strandedness
-    ch_cat_fastq
-        .branch {
-            meta, fastq ->
-                auto_strand : meta.strandedness == 'auto'
-                    return [ meta, fastq ]
-                known_strand: meta.strandedness != 'auto'
-                    return [ meta, fastq ]
-        }
-        .set { ch_strand_fastq }
-
-    //
-    // SUBWORKFLOW: Sub-sample FastQ files and pseudoalign with Salmon to auto-infer strandedness
-    //
-    // Return empty channel if ch_strand_fastq.auto_strand is empty so salmon index isn't created
-    PREPARE_GENOME.out.fasta
-        .combine(ch_strand_fastq.auto_strand)
-        .map { it.first() }
-        .first()
-        .set { ch_genome_fasta }
-
-    FASTQ_SUBSAMPLE_FQ_SALMON (
-        ch_strand_fastq.auto_strand,
-        ch_genome_fasta,
-        PREPARE_GENOME.out.transcript_fasta,
-        PREPARE_GENOME.out.gtf,
-        PREPARE_GENOME.out.salmon_index,
-        !params.salmon_index && !('salmon' in prepareToolIndices)
-    )
-    ch_versions = ch_versions.mix(FASTQ_SUBSAMPLE_FQ_SALMON.out.versions)
-
-    FASTQ_SUBSAMPLE_FQ_SALMON
-        .out
-        .json_info
-        .join(ch_strand_fastq.auto_strand)
-        .map { meta, json, reads ->
-            return [ meta + [ strandedness: WorkflowRnaseq.getSalmonInferredStrandedness(json) ], reads ]
-        }
-        .mix(ch_strand_fastq.known_strand)
-        .set { ch_strand_inferred_fastq }
-
     //
     // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore!
     //
@@ -295,7 +254,7 @@ workflow RNASEQ {
     ch_trim_read_count     = Channel.empty()
     if (params.trimmer == 'trimgalore') {
         FASTQ_FASTQC_UMITOOLS_TRIMGALORE (
-            ch_strand_inferred_fastq,
+            ch_cat_fastq,
             params.skip_fastqc || params.skip_qc,
             params.with_umi,
             params.skip_umi_extract,
@@ -316,7 +275,7 @@ workflow RNASEQ {
     //
     if (params.trimmer == 'fastp') {
         FASTQ_FASTQC_UMITOOLS_FASTP (
-            ch_strand_inferred_fastq,
+            ch_cat_fastq,
             params.skip_fastqc || params.skip_qc,
             params.with_umi,
             params.skip_umi_extract,
@@ -388,6 +347,48 @@ workflow RNASEQ {
         ch_sortmerna_multiqc = SORTMERNA.out.log
         ch_versions = ch_versions.mix(SORTMERNA.out.versions.first())
     }
+    
+    //
+    // SUBWORKFLOW: Sub-sample FastQ files and pseudoalign with Salmon to auto-infer strandedness
+    //
+    
+    // Branch FastQ channels if 'auto' specified to infer strandedness
+    ch_filtered_reads
+        .branch {
+            meta, fastq ->
+                auto_strand : meta.strandedness == 'auto'
+                    return [ meta, fastq ]
+                known_strand: meta.strandedness != 'auto'
+                    return [ meta, fastq ]
+        }
+        .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
+        .combine(ch_strand_fastq.auto_strand)
+        .map { it.first() }
+        .first()
+        .set { ch_genome_fasta }
+
+    FASTQ_SUBSAMPLE_FQ_SALMON (
+        ch_strand_fastq.auto_strand,
+        ch_genome_fasta,
+        PREPARE_GENOME.out.transcript_fasta,
+        PREPARE_GENOME.out.gtf,
+        PREPARE_GENOME.out.salmon_index,
+        !params.salmon_index && !('salmon' in prepareToolIndices)
+    )
+    ch_versions = ch_versions.mix(FASTQ_SUBSAMPLE_FQ_SALMON.out.versions)
+
+    FASTQ_SUBSAMPLE_FQ_SALMON
+        .out
+        .json_info
+        .join(ch_strand_fastq.auto_strand)
+        .map { meta, json, reads ->
+            return [ meta + [ strandedness: WorkflowRnaseq.getSalmonInferredStrandedness(json) ], reads ]
+        }
+        .mix(ch_strand_fastq.known_strand)
+        .set { ch_strand_inferred_filtered_fastq }
 
     //
     // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with Salmon
@@ -402,7 +403,7 @@ workflow RNASEQ {
     ch_aligner_clustering_multiqc = Channel.empty()
     if (!params.skip_alignment && params.aligner == 'star_salmon') {
         ALIGN_STAR (
-            ch_filtered_reads,
+            ch_strand_inferred_filtered_fastq,
             PREPARE_GENOME.out.star_index.map { [ [:], it ] },
             PREPARE_GENOME.out.gtf.map { [ [:], it ] },
             params.star_ignore_sjdbgtf,
@@ -521,7 +522,7 @@ workflow RNASEQ {
     ch_rsem_multiqc = Channel.empty()
     if (!params.skip_alignment && params.aligner == 'star_rsem') {
         QUANTIFY_RSEM (
-            ch_filtered_reads,
+            ch_strand_inferred_filtered_fastq,
             PREPARE_GENOME.out.rsem_index,
             PREPARE_GENOME.out.fasta.map { [ [:], it ] }
         )
@@ -555,7 +556,7 @@ workflow RNASEQ {
     ch_hisat2_multiqc = Channel.empty()
     if (!params.skip_alignment && params.aligner == 'hisat2') {
         FASTQ_ALIGN_HISAT2 (
-            ch_filtered_reads,
+            ch_strand_inferred_filtered_fastq,
             PREPARE_GENOME.out.hisat2_index.map { [ [:], it ] },
             PREPARE_GENOME.out.splicesites.map { [ [:], it ] },
             PREPARE_GENOME.out.fasta.map { [ [:], it ] }
@@ -826,7 +827,7 @@ workflow RNASEQ {
        }
 
         QUANTIFY_PSEUDO_ALIGNMENT (
-            ch_filtered_reads,
+            ch_strand_inferred_filtered_fastq,
             ch_pseudo_index,
             ch_dummy_file,
             PREPARE_GENOME.out.gtf,

From 282e972219d55fbd921639dd2bdf3db80de52c0f Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Thu, 4 Jan 2024 16:53:15 +0000
Subject: [PATCH 3/6] [skip ci] bump versions

---
 CHANGELOG.md              | 2 +-
 assets/multiqc_config.yml | 2 +-
 nextflow.config           | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8614fd74e..13d46a64a 100644
--- a/CHANGELOG.md
+++ b/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).
 
-## v3.14.0dev - [date]
+## v3.14.0 - 2024-01-05
 
 ### Credits
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 3dfec8dcb..e738f4854 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnaseq/tree/dev" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/3.13.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.14.0" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/3.14.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-rnaseq-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 9a4276636..f4d9f87e2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -322,7 +322,7 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.14.0dev'
+    version         = '3.14.0'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 

From 213d904a320abaa1199b52c2edacd8e3346fafb0 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Thu, 4 Jan 2024 18:18:54 +0000
Subject: [PATCH 4/6] Fix conditional publishing to avoid empty dirs

---
 conf/modules.config | 97 ++++++++++++++++++++++++---------------------
 1 file changed, 51 insertions(+), 46 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 466521922..1257ea68c 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -39,9 +39,9 @@ process {
 process {
     withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' {
         publishDir = [
-            path: { "${params.outdir}/genome" },
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
@@ -51,26 +51,26 @@ process {
 
     withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
         publishDir = [
-            path: { "${params.outdir}/genome/index" },
+            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
     withName: 'GFFREAD' {
         ext.args   = '--keep-exon-attrs -F -T'
         publishDir = [
-            path: { "${params.outdir}/genome" },
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
     withName: 'HISAT2_EXTRACTSPLICESITES' {
         publishDir = [
-            path: { "${params.outdir}/genome/index" },
+            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
@@ -80,68 +80,68 @@ process {
                 params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}": ''
         ].join(' ').trim() }
         publishDir = [
-            path: { "${params.outdir}/genome/index" },
+            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
     withName: 'KALLISTO_INDEX' {
         ext.args   = params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}" : ''
         publishDir = [
-            path: { "${params.outdir}/genome/index" },
+            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
     withName: 'RSEM_PREPAREREFERENCE_GENOME' {
         ext.args   = '--star'
         publishDir = [
-            path: { "${params.outdir}/genome/index" },
+            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
     withName: 'GTF2BED' {
         publishDir = [
-            path: { "${params.outdir}/genome" },
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
     withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
         publishDir = [
-            path: { "${params.outdir}/genome" },
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
     withName: 'GTF_FILTER' {
         ext.args   = { params.skip_gtf_transcript_filter ?: '--skip_transcript_id_check' }
         publishDir = [
-            path: { "${params.outdir}/genome" },
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
     withName: 'CUSTOM_GETCHROMSIZES' {
         publishDir = [
-            path: { "${params.outdir}/genome" },
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
 
     withName: 'CAT_FASTQ' {
         publishDir = [
-            path: { "${params.outdir}/fastq" },
+            path: { params.save_merged_fastq ? "${params.outdir}/fastq" : params.outdir },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_merged_fastq ? filename : null }
+            saveAs: { filename -> (filename.endsWith('.fastq.gz') && params.save_merged_fastq) ? filename : null }
         ]
     }
 }
@@ -151,9 +151,9 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
         withName: '.*:PREPARE_GENOME:BBMAP_BBSPLIT' {
             ext.args   = 'build=1'
             publishDir = [
-                path: { "${params.outdir}/genome/index" },
+                path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+                saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
             ]
         }
     }
@@ -228,7 +228,7 @@ if (!params.skip_trimming) {
                         pattern: "*.{html,zip}"
                     ],
                     [
-                        path: { "${params.outdir}/${params.trimmer}" },
+                        path: { params.save_trimmed ? "${params.outdir}/${params.trimmer}" : params.outdir },
                         mode: params.publish_dir_mode,
                         pattern: "*.fq.gz",
                         saveAs: { params.save_trimmed ? it : null }
@@ -259,7 +259,7 @@ if (!params.skip_trimming) {
                         pattern: "*.log"
                     ],
                     [
-                        path: { "${params.outdir}/${params.trimmer}" },
+                        path: { params.save_trimmed ? "${params.outdir}/${params.trimmer}" : params.outdir },
                         mode: params.publish_dir_mode,
                         pattern: "*.fastq.gz",
                         saveAs: { params.save_trimmed ? it : null }
@@ -286,7 +286,7 @@ if (params.with_umi && !params.skip_umi_extract) {
                     pattern: "*.log"
                 ],
                 [
-                    path: { "${params.outdir}/umitools" },
+                    path: { params.save_umi_intermeds ? "${params.outdir}/umitools" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: "*.fastq.gz",
                     saveAs: { params.save_umi_intermeds ? it : null }
@@ -311,7 +311,7 @@ if (!params.skip_bbsplit) {
                     pattern: '*.txt'
                 ],
                 [
-                    path: { "${params.outdir}/bbsplit" },
+                    path: { params.save_bbsplit_reads ? "${params.outdir}/bbsplit" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.fastq.gz',
                     saveAs: { params.save_bbsplit_reads ? it : null }
@@ -332,7 +332,7 @@ if (params.remove_ribo_rna) {
                     pattern: "*.log"
                 ],
                 [
-                    path: { "${params.outdir}/sortmerna" },
+                    path: { params.save_non_ribo_reads ? "${params.outdir}/sortmerna" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: "*.fastq.gz",
                     saveAs: { params.save_non_ribo_reads ? it : null }
@@ -360,7 +360,9 @@ if (!params.skip_alignment) {
         withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
             ext.prefix = { "${meta.id}.sorted" }
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
+                path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
+                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
+                    ) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
                 mode: params.publish_dir_mode,
                 pattern: "*.bam",
                 saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
@@ -372,6 +374,9 @@ if (!params.skip_alignment) {
         withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
             ext.args   = { params.bam_csi_index ? '-c' : '' }
             publishDir = [
+                path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
+                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
+                    ) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
                 path: { "${params.outdir}/${params.aligner}" },
                 mode: params.publish_dir_mode,
                 pattern: "*.{bai,csi}",
@@ -438,7 +443,7 @@ if (!params.skip_alignment) {
                         pattern: '*.tsv'
                     ],
                     [
-                        path: { "${params.outdir}/${params.aligner}" },
+                        path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                         mode: params.publish_dir_mode,
                         pattern: '*.bam',
                         saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
@@ -450,7 +455,7 @@ if (!params.skip_alignment) {
                 ext.args   = { params.bam_csi_index ? '-c' : '' }
                 ext.prefix = { "${meta.id}.umi_dedup.sorted" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
+                    path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.{bai,csi}',
                     saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
@@ -556,13 +561,13 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                     pattern: '*.{out,tab}'
                 ],
                 [
-                    path: { "${params.outdir}/${params.aligner}" },
+                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.bam',
                     saveAs: { params.save_align_intermeds ? it : null }
                 ],
                 [
-                    path: { "${params.outdir}/${params.aligner}/unmapped" },
+                    path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.fastq.gz',
                     saveAs: { params.save_unaligned ? it : null }
@@ -611,7 +616,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                 ext.args   = '-n'
                 ext.prefix = { "${meta.id}.umi_dedup.transcriptome" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.bam',
                     saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
@@ -627,7 +632,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                         pattern: '*.log'
                     ],
                     [
-                        path: { "${params.outdir}/${params.aligner}" },
+                        path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                         mode: params.publish_dir_mode,
                         pattern: '*.bam',
                         saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
@@ -638,7 +643,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
             withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
                 ext.prefix = { "${meta.id}.transcriptome.sorted" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.bam',
                     saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
@@ -647,7 +652,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
 
             withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.bai',
                     saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
@@ -657,7 +662,7 @@ 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.outdir}/${params.aligner}/samtools_stats" },
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.{stats,flagstat,idxstats}',
                     saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
@@ -678,7 +683,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                         pattern: '*.tsv'
                     ],
                     [
-                        path: { "${params.outdir}/${params.aligner}" },
+                        path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                         mode: params.publish_dir_mode,
                         pattern: '*.bam',
                         saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
@@ -688,7 +693,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
 
             withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.bai',
                     saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
@@ -747,7 +752,7 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
                     pattern: "*.{stat,results}"
                 ],
                 [
-                    path: { "${params.outdir}/${params.aligner}" },
+                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: "*.bam",
                     saveAs: { params.save_align_intermeds ? it : null }
@@ -804,13 +809,13 @@ if (!params.skip_alignment && params.aligner == 'hisat2') {
                     pattern: '*.log'
                 ],
                 [
-                    path: { "${params.outdir}/${params.aligner}" },
+                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.bam',
                     saveAs: { params.save_align_intermeds ? it : null }
                 ],
                 [
-                    path: { "${params.outdir}/${params.aligner}/unmapped" },
+                    path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
                     mode: params.publish_dir_mode,
                     pattern: '*.fastq.gz',
                     saveAs: { params.save_unaligned ? it : null }

From 7843299751f1a64fb3d5a526a06f22a2dcaec686 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Thu, 4 Jan 2024 18:27:03 +0000
Subject: [PATCH 5/6] [skip ci] update changelog

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 13d46a64a..8a066269d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,9 +22,10 @@ Special thanks to the following for their contributions to the release:
 - [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling
 - [PR #1141](https://github.com/nf-core/rnaseq/pull/1141) - Important! Template update for nf-core/tools v2.11
 - [PR #1143](https://github.com/nf-core/rnaseq/pull/1143) - Move fasta check back to Groovy ([#1142](https://github.com/nf-core/rnaseq/issues/1142))
-- [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners
+- [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners ([#1111](https://github.com/nf-core/rnaseq/issues/1111))
 - [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Fix and patch version commands for Fastp, FastQC and UMI-tools modules ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
 - [PR #1150](https://github.com/nf-core/rnaseq/pull/1150) - Be more flexible on attribute values in GTFs ([#1132](https://github.com/nf-core/rnaseq/issues/1132))
+- [PR #1154](https://github.com/nf-core/rnaseq/pull/1154) - Prerelease 3.14.0 fixes ([#1111](https://github.com/nf-core/rnaseq/issues/1111), [#1153](https://github.com/nf-core/rnaseq/issues/1153))
 
 ### Parameters
 

From f06f298abe39a6efd5e1d2f31e7ea1e09911dd2e Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Fri, 5 Jan 2024 09:49:33 +0000
Subject: [PATCH 6/6] Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 CHANGELOG.md        | 2 +-
 conf/modules.config | 3 +--
 workflows/rnaseq.nf | 4 +++-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 73b3e39ac..7a0938d17 100644
--- a/CHANGELOG.md
+++ b/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
 
diff --git a/conf/modules.config b/conf/modules.config
index 1257ea68c..16d635cdb 100644
--- a/conf/modules.config
+++ b/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 }
diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
index 178d9003a..9250125dc 100755
--- a/workflows/rnaseq.nf
+++ b/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()