salmon_summarizedexperiment.r failing with test data

[svenbioinf]

Description of the bug

Hello,
I am running into an error using the latest nf-core/rnaseq pipeline with test-data from the test-datasets repository. Below is an reproducible example:

Command used and terminal output

nextflow run nf-core/rnaseq --outdir out/ --input https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_test.csv 
--skip_alignment --pseudo_aligner salmon -profile singularity 
--max_cpus 8 --max_memory 40.GB 
--transcript_fasta https://github.com/nf-core/test-datasets/raw/rnaseq/reference/transcriptome.fasta 
--fasta https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fasta 
--gtf https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz
Error:
ColData not avaliable NULL
  Error in rbind(deparse.level, ...) : 
    numbers of columns of arguments do not match
Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv)` terminated with an error exit status (1)

Command executed:

  salmon_summarizedexperiment.r \
      NULL \
      salmon.merged.transcript_counts.tsv \
      salmon.merged.transcript_tpm.tsv

Relevant files

No response

System information

nf-core/rnaseq v3.10.1-g6e1e448
N E X T F L O W ~ version 22.10.6
Singularity
Linux
Ubuntu 22.04

[drpatelh]

Thanks for reporting @svenbioinf ! @MatthiasZepper has fixed this for you on the dev branch if you would like to test.

nextflow pull nf-core/rnaseq -r dev
nextflow run <YOUR_ORIGINAL_COMMAND> -r dev

Will close this for now but feel free to re-open if the problem persists.