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nf-core / nanoseq

Nanopore demultiplexing, QC and alignment pipeline
https://nf-co.re/nanoseq
MIT License
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Pairing between sample and genome is ignored for demultiplexed reads (cDNA mode) #254

Open nschan opened 1 year ago

nschan commented 1 year ago

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 commented 1 year ago

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

nschan commented 8 months ago

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