Bug with aggregation of Quast reports

[travis-m-blimkie]

Description of the bug

Running bacpaq on Illumina reads seems to complete without issue, however the output aggregate report for Quast only contains the results for a single sample.

Command used and terminal output

Script for slurm submission:

#!/bin/bash
#SBATCH --time=12:00:00
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --account=def-ahylee
#SBATCH --output=Logs/slurm-%j-_nextflow_test_run.out

module load StdEnv/2023 nextflow/24.04.4 apptainer/1.2.4

nextflow run cidgoh/bacpaq \
   -r v1.0.1 \
   -profile cedar,singularity \
   --account df-ahylee \
   --input sample_sheet_test_25.csv \
   --outdir Nextflow_results_test_25 \
   --genome_size 5700000 \
   --depth_cut_off 40 \
   --trim_tool trimmomatic \
   --skip_kraken2 true \
   --confindr_db /home/tblimkie/.confindr_db \
   --skip_taxonomy_qc true \
   --skip_dehosting true \
   --sr_assembler spades \
   --skip_porechop true \
   --skip_subsampling true \
   --skip_pycoqc true \
   --skip_checkm true \
   --skip_busco true \
   --skip_gene_annotation true \
   --skip_prokka true \
   --skip_bakta true \
   --skip_abricate true \
   --skip_amr_annotation true \
   --skip_rgi true \
   --skip_abritamr true \
   --skip_amrfinderplus true \
   --skip_phage_annotation true \
   --skip_mobsuite true \
   --skip_plasmidfinder true \
   --skip_crispr true \
   --skip_roary true \
   --skip_pirate true

Relevant files

nextflow.log quast.log report.zip

System information

Nextflow version: 24.04.4 Hardware: Cedar Executor: slurm Container engine: singularity OS: Alma Linux Version of bacpaq: v1.0.1