Fix nf-core#975

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).
 
-## [[3.11.0](https://github.com/nf-core/rnaseq/releases/tag/3.11.0)] - 2023-03-27
+## [[3.11.0](https://github.com/nf-core/rnaseq/releases/tag/3.11.0)] - 2023-03-29
 
 ### Credits
 
@@ -24,16 +24,17 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
   - Users can now select between `--trimmer trimgalore` (default) and `--trimmer fastp`.
   - Trim Galore! specific pipeline parameters have been deprecated: `--clip_r1`, `--clip_r2`, `--three_prime_clip_r1`, `--three_prime_clip_r2` and `--trim_nextseq`
   - Any additional options can now be specified via the `--extra_trimgalore_args` and `--extra_fastp_args` parameters, respectively.
-- [[#663](https://github.com/nf-core/rnaseq/pull/663)] - Alternative trimming step for polyA/T removal
-- [[#781](https://github.com/nf-core/rnaseq/pull/781)] - Add Warning for poly(A) libraries
-- [[#878](https://github.com/nf-core/rnaseq/pull/878)] - Allow tabs in fasta header when creating decoys for salmon index
-- [[#931](https://github.com/nf-core/rnaseq/pull/931)] - Save transcriptome BAM files when using `--save_umi_intermeds` / `--save_align_intermeds`
+- [[#663](https://github.com/nf-core/rnaseq/issues/663)] - Alternative trimming step for polyA/T removal
+- [[#781](https://github.com/nf-core/rnaseq/issues/781)] - Add Warning for poly(A) libraries
+- [[#878](https://github.com/nf-core/rnaseq/issues/878)] - Allow tabs in fasta header when creating decoys for salmon index
+- [[#931](https://github.com/nf-core/rnaseq/issues/931)] - Save transcriptome BAM files when using `--save_umi_intermeds` / `--save_align_intermeds`
 - [[#934](https://github.com/nf-core/rnaseq/pull/934)] - Union of `ext.args` and `params.extra_star_align_args` prevents parameter clashes in the STAR module
-- [[#940](https://github.com/nf-core/rnaseq/issues/940)] - Bugfix in `salmon_summarizedexperiment.r` to ensure `rbind` doesn't fail when `rowdata` has no `tx` column. See ([[#941](https://github.com/nf-core/rnaseq/pull/941)]) for details.
+- [[#940](https://github.com/nf-core/rnaseq/issues/940)] - Bugfix in `salmon_summarizedexperiment.r` to ensure `rbind` doesn't fail when `rowdata` has no `tx` column.
 - [[#944](https://github.com/nf-core/rnaseq/issues/944)] - Read clipping using clip_r1, clip_r2, three_prime_clip_r1, three_prime_clip_r2 disabled in 3.10
 - [[#956](https://github.com/nf-core/rnaseq/pull/956)] - Implement 'auto' as default strandedness argument in `fastq_dir_to_samplesheet.py` script
-- [[#960](https://github.com/nf-core/rnaseq/pull/960)] - Failure with awsbatch when running processes that are using `executor: local`
-- [[#961](https://github.com/nf-core/rnaseq/pull/961)] - Add warnings to STDOUT for all skipped and failed strandedness check samples
+- [[#960](https://github.com/nf-core/rnaseq/issues/960)] - Failure with awsbatch when running processes that are using `executor: local`
+- [[#961](https://github.com/nf-core/rnaseq/issues/961)] - Add warnings to STDOUT for all skipped and failed strandedness check samples
+- [[#975](https://github.com/nf-core/rnaseq/issues/975)] - `SALMON_INDEX` runs when using `--aligner star_rsem` even if samples have explicit strandedness
 - Remove HISAT2 from automated AWS full-sized tests
 
 ### Parameters

workflows/rnaseq.nf

@@ -243,9 +243,15 @@ workflow RNASEQ {
     //
     // SUBWORKFLOW: Sub-sample FastQ files and pseudo-align 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() }
+        .set { ch_genome_fasta }
+
     FASTQ_SUBSAMPLE_FQ_SALMON (
         ch_strand_fastq.auto_strand,
-        PREPARE_GENOME.out.fasta,
+        ch_genome_fasta,
         PREPARE_GENOME.out.transcript_fasta,
         PREPARE_GENOME.out.gtf,
         PREPARE_GENOME.out.salmon_index,