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nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
https://nf-co.re/taxprofiler
MIT License
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taxprofiler krona output files missing #479

Closed aslangabriel99 closed 5 months ago

aslangabriel99 commented 5 months ago

Description of the bug

I ran the pipeline with the command "nextflow run nf-core/taxprofiler -r 1.1.0 -profile docker \ --input samplesheet_06YRkraken.csv --databases database_06YRkraken.csv --outdir ./06YRkrakenkaijuresults \ --perform_shortread_qc \ --perform_shortread_hostremoval --hostremoval_reference OR666647_1_DHAV3.fna \ --perform_runmerging --save_runmerged_reads \ --run_kraken2 --run_kaiju \ --run_profile_standardisation \ --max_cpus 11 --max_memory '125.GB" , following the turotial. But there are no krona output files found.

Command used and terminal output

No response

Relevant files

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System information

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jfy133 commented 5 months ago

Hi @aslangabriel99

Unless I'm missing something, you didn't supply --run_krona.

Please check the parameter documentation here: https://nf-co.re/taxprofiler/1.1.6/parameters#run_krona

Closing now, but feel free to re-open if I did indeed miss something