Filenames of output file?

[Thomieh73]

Description of the bug

Hi,
I ran Taxprofiler and I notice that my sample names are changed in a way that I find a bit odd.

This is original file name as I give it in the samplesheet.

DNA_H1H_17_A5_1.fq.gz
DNA_H1H_17_A5_2.fq.gz

and it becomes:

DNA_H1H_17_A5_DNA_H1H_17.unmapped_1.fastq.gz
DNA_H1H_17_A5_DNA_H1H_17.unmapped_2.fastq.gz

Where does the repeat "DNA_H1H_17" come from.

This was my command to run the job:

nextflow run nf-core/taxprofiler -r 1.1.8 -profile apptainer \
-c saga_taxprofiler.config -work-dir $USERWORK/taxprofiler -resume \
--input taxprofiler_samplesheet.csv --databases ./databases.csv \
--outdir ../../results/20240911_TP_results \
--perform_shortread_qc \
--shortread_qc_minlength 50 \
--perform_shortread_complexityfilter \
--perform_shortread_hostremoval \
--hostremoval_reference ../../viral_mask_results/masked_host_db/combined_hosts_phix.fna.gz \
--shortread_hostremoval_index ../../viral_mask_results/masked_host_db \
--run_kraken2 \
--run_bracken \
--run_motus \
--motus_save_mgc_read_counts \
--run_profile_standardisation \
--save_analysis_ready_fastqs \
--max_cpus 32

and my sample sheet looks like this:

sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
DNA_H1H_10_A1,DNA_H1H_10,ILLUMINA,/cluster/projects/nn10070k/projects/phagedrive/pd_data_control/data/DNA_H1H_10_A1_1.fq.gz,/cluster/projects/nn10070k/projects/phagedrive/pd_data_control/data/DNA_H1H_10_A1_2.fq.gz,
DNA_H1H_10_B1,DNA_H1H_10,ILLUMINA,/cluster/projects/nn10070k/projects/phagedrive/pd_data_control/data/DNA_H1H_10_B1_1.fq.gz,/cluster/projects/nn10070k/projects/phagedrive/pd_data_control/data/DNA_H1H_10_B1_2.fq.gz,

Command used and terminal output

nextflow run nf-core/taxprofiler -r 1.1.8 -profile apptainer \
-c saga_taxprofiler.config -work-dir $USERWORK/taxprofiler -resume \
--input taxprofiler_samplesheet.csv --databases ./databases.csv \
--outdir ../../results/20240911_TP_results \
--perform_shortread_qc \
--shortread_qc_minlength 50 \
--perform_shortread_complexityfilter \
--perform_shortread_hostremoval \
--hostremoval_reference ../../viral_mask_results/masked_host_db/combined_hosts_phix.fna.gz \
--shortread_hostremoval_index ../../viral_mask_results/masked_host_db \
--run_kraken2 \
--run_bracken \
--run_motus \
--motus_save_mgc_read_counts \
--run_profile_standardisation \
--save_analysis_ready_fastqs \
--max_cpus 32

Relevant files

No response

System information

No response

[sofstam]

Hello! The name is coming from the configuration of the modules. We combine the sample and run_accession.

[Thomieh73]

Ah. now I understand it. It should then not happen if I keep the run_accessions blank. I will check that. :-)

[sofstam]

The column sample and run_accession are sample identifiers (sample name and run id) and I do not think you can keep none of them empty.

[sofstam]

Will close this for now but feel free to reopen it if you have any questions :)