Pipeline fails when "test.fa" is missing

[travis-m-blimkie]

Description of the bug

Running the pipeline on "real" data returns an error, with the log showing the cause as a missing file (test.fa). Creating this file in the current/working directory (e.g. touch /scratch/tblimkie/Testing_bacpaq/test.fa) resolves the error, allowing the pipeline to proceed.

Command used and terminal output

#!/bin/bash

# Load modules on cedar, after moving to an interactive node via `salloc`
module purge && module load StdEnv/2023 nextflow/24.04.4 apptainer/1.2.4

nextflow -log Logs/nextflow_test_run.log run cidgoh/bacpaq \
   -r v1.0.1 \
   -profile cedar,singularity \
   --account df-ahylee \
   --input sample_sheet_test.csv \
   --outdir Nextflow_results_test \
   --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_test_run.log
sample_sheet_test.csv

System information

Nextflow: 24.04.4
Hardware: Cedar
Executor: Local (salloc)
Container: Singularity
OS: Linux
Version of bacpaq: v1.0.1

[travis-m-blimkie]

I'm going to try to fix this...