DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER not working with special characters in sample names

[fhausmann]

Description of the bug

The stage DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER is not running when special characters, such as '-' are in the sample names.

The reason is that counts are converted to a data.frame, which modifies header names. Therefore, sample names are not matching to the counts header/column names afterward.

Command used and terminal output

Error in DRIMSeq::dmDSdata(counts = counts, samples = samps) : 
    all(samples$sample_id %in% colnames(counts)) is not TRUE
  Calls: <Anonymous> -> stopifnot
  Execution halted

Relevant files

No response

System information

• Nextflow version: 24.04.2
• Hardware: HPC
• Executor: local
• Container engine: Docker
• OS: Linux
• Version of nf-core/rnasplice: 1.0.4