Pairing between sample and genome is ignored for demultiplexed reads (cDNA mode)

[nschan]

Description of the bug

When providing several samples that should be mapped to different genomes in a samplesheet, the pairing between sample (group) and genome is ignored.

Expected behaviour:
Reads from each group are mapped to the genome provided in the same row in "fasta".

Actual behaviour:
The reads and genomes are matched in a different order, presumably based on when they pass through the pipeline.

Parameters:
protocol: 'cDNA'
skip_demultiplexing: true
skip_modification_analysis: true
skip_fusion_analysis: true

It would be helpful if this behaviour was mentioned in the documentation, since it is not really obvious from the samplesheet layout and seems to be even suggested in the "With demultiplexing" section of the Usage documentation

Command used and terminal output

No response

Relevant files

No response

System information

Nextflow version: nextflow 23.08.1-edge
Hardware: HPC
Executor: slurm
Container engine: charliecloud
OS: SUSE
Pipeline version: nanoseq v3.1.0

[nschan]

Actually, this turned out to be a problem with my samplesheet, sorry.

[nschan]

I would like to reopen the issue, since I do not think it is an issue with my samplesheet.
Rather, it seems like #nf-core/nanoseq/blob/master/subworkflows/local/align_minimap2.nf#L21 does cross genome and fastq channels, but as far as I understand PREPARE_GENOME does not return the sample name / meta in the ch_fastq #nf-core/nanoseq/blob/master/subworkflows/local/prepare_genome.nf#L29