Naming of the output files

[heksaani]

Hey I have this weird problem I've described here

But in short my problem is that the workflow produces following folders for two test samples (when given the folder path as input parameter)

/results/irma_results_2025-09-01_13-54/test_sample1/
/results/irma_results_2025-09-01_13-54/test_sample2/

in those folders are IRMA’s results.

However, the FASTA files in the amended_consensus/ subfolder are misnamed.

Running IRMA directly on the command line / or with conda produces segment-specific names:

/results/irma_results_2025-09-01_13-54/test_sample1/amended_consensus/test_sample1_HA.fa
/results/irma_results_2025-09-01_13-54/test_sample1/amended_consensus/test_sample1_NA.fa

But Running IRMA via Nextflow produces generic numbered names:

amended_consensus/test_sample1_1.fa
amended_consensus/test_sample1_2.fa

The segment names (_HA, _NA) are lost in the Nextflow run. This naming is important for downstream analyses, because these suffixes indicate the viral segment in each FASTA file.

Can someone explain why this could happen and what should I do differently to prevent the mismatch in naming ?

[bentsherman]

I will respond in the original post