Sample name not included in consensus fasta file

[avantonder]

Operating System

Other Linux (please specify below)

Other Linux

Redhat

Workflow Version

v1.1.1

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-bacterial-genomes --fastq data/fastq_pass/ --reference_based_assembly --reference GCF_900205735.1_N16961_v2_genomic.fna --sample_sheet samplesheet_epi2me.csv -profile singularity -c cambridge.config -resume

Workflow Execution - CLI Execution Profile

singularity

What happened?

The pipeline ran successfully but the consensus fasta files created by the pipeline have the reference name and basecaller model in the fasta header instead of the sample id. This is not particularly helpful for building alignments to create phylogenetic trees.

Relevant log output

grep ">" CTMA_1402.medaka.fasta

>NZ_LT906615.1 [email protected]

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

other (please describe below)

Other demo data information

Not tested

[cjalder]

Hi @avantonder thanks for raising this issue. In your example what would you propose, something like the following:
>CTMA_1402 NZ_LT906615.1 [email protected]?

[avantonder]

@cjalder Yes, this would work