Salmon index is not stored when using --save_reference

[SuhasSrinivasan]

Description of the bug

Dear Developers,

Thank you for helping with the issues.

When using the --save_reference parameter, the Salmon index is not stored in the genome directory.
The STAR index is stored (and even RSEM see #1547), but not Salmon.

Request

It will be helpful if Salmon index can be stored, so that it can be passed for future runs, thereby saving time.

Command used and terminal output

nextflow run nf-core/rnaseq 
-profile singularity 
--save_reference \
--input /mnt/storage/projects/r2/rna_initial/fastqs/samples.csv \
--outdir  /mnt/storage/projects/r2/rna_initial/ \
--gtf /mnt/storage/projects/reference/rna/gencode.v47.primary_assembly.annotation.gtf \
--fasta /mnt/storage/projects/reference/rna/GRCh38.primary_assembly.genome.fa

Relevant files

Contents of the genome directory after a successful pipeline run.

$ ls -lah
total 2.3G
drwxrwxr-x 4 userx userx 4.0K Apr 21 02:26 .
drwxrwxr-x 8 userx userx 4.0K Apr 22 18:17 ..
-rw-rw-r-- 1 userx userx 546M Apr 21 00:31 genome.transcripts.fa
-rw-rw-r-- 1 userx userx 6.4K Apr 21 00:16 GRCh38.primary_assembly.genome.fa.fai
-rw-rw-r-- 1 userx userx 3.2K Apr 21 00:16 GRCh38.primary_assembly.genome.fa.sizes
-rw-rw-r-- 1 userx userx  45M Apr 21 00:16 GRCh38.primary_assembly.genome.filtered.bed
-rw-rw-r-- 1 userx userx 1.7G Apr 21 00:16 GRCh38.primary_assembly.genome.filtered.gtf
drwxrwxr-x 3 userx userx 4.0K Apr 21 02:26 index
drwxrwxr-x 2 userx userx 4.0K Apr 21 00:31 rsem

System information

Version of nf-core/rnaseq: 3.18.0
Nextflow version: v24.10.5
Container engine: singularity-ce version 4.1.2-jammy
OS: Ubuntu 22.04.5 LTS x86_64
Executor: Local
Hardware: Desktop

[pinin4fjords]

Default behaviour is to run Salmon in alignment-based mode, which does not involve an index, so that will not be generated. If you specify pseudo_aligner, then Salmon will (also) be run in mapping-based mode which does involve the creation of an index, which will be stored.

[SuhasSrinivasan]

Thank you for the clarification!