--bam_csi_index error generated if --skip_alignment specified

[baptisteImbert]

Description of the bug

Hi, the following bug was discussed on the Slack #rnaseq channel (4th March) and a workaround was identified.
When trying to use salmon pseudo-mapping quantification, an error asking to add "--bam_csi_index" because of long chromosomes will show up, despite the parameter being already mentionned.
This issue does not appear on v3.5.

Command used and terminal output

nextflow run nf-core/rnaseq -profile docker --input samplesheet.csv --fasta psat_genome.fa --gtf psat_annotation.gtf --pseudo_aligner salmon --skip_alignment --bam_csi_index --outdir results_rnaseq/henriet2019_sample


  Contig longer than 512000000bp found in reference genome!

  chr5LG3: 579269071

  Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.

  Please see:
  https://github.com/nf-core/rnaseq/issues/744

Relevant files

No response

System information

Nextflow version 21.10.6
nf-core/rnaseq 3.6

[drpatelh]

Fixed in #811