MultiQC Input File Name Collision

[rvijay-seqcoast]

Description of the bug

I am running into an issue with the generation of the MultiQC report in the bacass pipeline. This process runs into an "input file name collision" error and is unable to complete the report. Specifically, this error appears to occur when processing multiple samples with hybrid or long-read assemblies, but it does not occur when running a single hybrid or long-read assembly or when processing single or multiple samples with short-read assemblies. I have attached the nextflow log file, parameter file, and sample sheet below of an example run that ran into this error.

Command used and terminal output

nextflow run 'https://github.com/nf-core/bacass'
		 -name assembly_5706_2
		 -params-file 'https://api.cloud.seqera.io/ephemeral/2xKzdXhAmBlQi4GLwrdd9Q.json'
		 -with-tower
		 -r 2.3.1
		 -profile docker



Error executing process > 'NFCORE_BACASS:BACASS:MULTIQC_CUSTOM (1)'

Caused by:
  Process `NFCORE_BACASS:BACASS:MULTIQC_CUSTOM` input file name collision -- There are multiple input files for each of the following file names: nanoplot/NanoStats_post_filtering.txt

Relevant files

nf-3DxU8NpOkvS2iG.log
5706_samples.csv
assembly_5706_2-params.json

System information

• Nextflow version: 24.10.0
  

• Hardware: AWS
  

• Executor: awsbatch
  

• Container engine: Docker
  

• OS: Linux
  

• Version of nf-core/bacass: 2.3.1