genome (Rnor_5.0) availble in AWS genomes but not listed in config

[adomingues]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/rnaseq pipeline documentation

Description of the bug

From reading the docs I assumed that any genome stored in AWS-iGenomes would be readily available when calling the pipeline, but at least one, Rnor_5.0, isn't.

https://github.com/nf-core/rnaseq/blob/master/conf/igenomes.config

Steps to reproduce

Genome is pre-downloaded but error also occours without setting --igenomes_base

1. Command line: nextflow run nf-core/rnaseq -r 3.1 --input "${PRJ_DATA}/raw/bayer_samplesheet.csv" --igenomes_base "/mnt/genomics/references" --genome "Rnor_5.0" -profile singularity --aligner "star_salmon" -with-dag --max_memory "40.GB"
2. See error:

=============================================================================
  Genome 'Rnor_5.0' not found in any config files provided to the pipeline.
  Currently, the available genome keys are:
  GRCh37, GRCh38, GRCm38, TAIR10, EB2, UMD3.1, WBcel235, CanFam3.1, GRCz10, BDGP6, EquCab2, EB1, Galgal4, Gm01, Mmul_1, IRGSP-1.0, CHIMP2.1.4, Rnor_6.0, R64-1-1, EF2, Sbi1, Sscrofa10.2, AGPv3, hg38, hg19, mm10, bosTau8, ce10, canFam3, danRer10, dm6, equCab2, galGal4, panTro4, rn6, sacCer3, susScr3
===================================================================================

Expected behaviour

The pipeline should be able to use any iGenomes available in AWS.

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file

System

• Hardware: Linux server
• Executor:
• OS: Ubuntu
• Version 20.04

Nextflow Installation

• Version: 21.04.0-edge.5543

Container engine

• Engine: Singularity
• version:
• Image tag: nfcore/rnaseq:3.1.0

[drpatelh]

Added in #642