A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I dont really get what I did wrong, so I am asking here. Error:
```-[nf-core/taxprofiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_TAXPROFILER:taxprofiler:STANDARDISATION_PROFILES:TAXPASTA_MERGE (6)'
Caused by:
  Process `NFCORE_TAXPROFILER:taxprofiler:STANDARDISATION_PROFILES:TAXPASTA_MERGE` input file name collision -- There are multiple input files for each of the following file names: sample13sr_sample13sr_k2_standard_20260226.bracken.tsv, sample14sr_sample14sr_k2_standard_20260226.bracken.tsv, sample19sr_sample19sr_k2_standard_20260226.bracken.tsv```
More info in the thread.

image.png

Command I used to start the pipeline:
```NXF_VER=25.04.6 nextflow run nf-core/taxprofiler -r 2.0.0 -profile cfc -c resources_taxprofiler.config --input samplesheet_taxprofiler.csv --databases databases_taxprofiler.csv --outdir results_taxprofiler --perform_longread_qc --run_kraken2 --run_bracken --run_profile_standardisation --run_krona -resume```
samplesheet:
```sample,run_accession,instrument_platform,fastq_1,fastq_2
sample13,sample13,OXFORD_NANOPORE,Q2SG66001AP_Sample_13_pass.fastq.gz,
sample14,sample14,OXFORD_NANOPORE,Q2SG66002A0_Sample_14_pass.fastq.gz,
sample15,sample15,OXFORD_NANOPORE,Q2SG66003A9_Sample_15_pass.fastq.gz,
sample17,sample17,OXFORD_NANOPORE,Q2SG66004AI_Sample_17_pass.fastq.gz,
sample19,sample19,OXFORD_NANOPORE,Q2SG66005AR_Sample_19_pass.fastq.gz,
sample12,sample12,OXFORD_NANOPORE,Q2SG66007AB_Sample_12_pass.fastq.gz,
sample13sr,sample13sr,ILLUMINA,Q2SG66001AP_Sample_13_S23_R1_001.fastq.gz,Q2SG66001AP_Sample_13_S23_R2_001.fastq.gz
sample14sr,sample14sr,ILLUMINA,Q2SG66002A0_Sample_14_S24_R1_001.fastq.gz,Q2SG66002A0_Sample_14_S24_R2_001.fastq.gz
sample19sr,sample19sr,ILLUMINA,Q2SG66005AR_Sample_19_S25_R1_001.fastq.gz,Q2SG66005AR_Sample_19_S25_R2_001.fastq.gz```
databases:
```tool,db_name,db_type,db_params,db_path
kraken2,k2_standard_20260226,,,k2_standard_20260226.tar.gz
bracken,k2_standard_20260226,short,;-r 150,k2_standard_20260226.tar.gz
kraken2,k2_nt_20230502,,,k2_nt_20230502.tar.gz
bracken,k2_nt_20230502,short,;-r 150,k2_nt_20230502.tar.gz
kraken2,k2_core_nt_20251015,,,k2_core_nt_20251015.tar.gz
bracken,k2_core_nt_20251015,short,;-r 150,k2_core_nt_20251015.tar.gz```

Could you test to change the name in bracken?

From documentation:

```Please note that names need to be unique across both kraken2 and bracken as well, even if re-using the same database.```

If this does not work, could you please share the command you are using?

Thanks thats likely it, I seem to have missed that. I'll test it out

Just a thought, probably <https://github.com/nf-core/taxprofiler/blob/fa1aab03875c090c0594af7c2bbe22ada6c12391/assets/schema_database.json#L58> didnt work as intended?

It seems so. Can you maybe create an issue for that?

Done: <https://github.com/nf-core/taxprofiler/issues/742>