Permission denied OR Command Error non-fastq files in fastq folder(s) in Module 4

[Merritt-Brian]

A recursive find is performed for pipeline ingestion at module 4 where it is attempting to find all seq_summary files in the fastq folder following standalone CLI or MinKNOW basecall analysis. Keeping this file in the fastq folder and not the run folder i.e. having multiple sequencing_summary.txt files causes potential issues .

Nanopolish log (Module 4)

[2021-04-29 21:00:57] SAMPLE NTC_NB01:------ processing nanopolish --------
[2021-04-29 21:00:57] SAMPLE NTC_NB01: Starting Module 4 Nanopolish
index: not enough arguments
/opt/basestack_consensus/sequencing_runs/example-run/sequencing_summary_FAN44250_77d58da2.txt: line 1: filename_fastq: command not found

Potentially the issue starts here https://github.com/jhuapl-bio/basestack_consensus/blob/main/pipeline_scripts/artic-module4-draft-consensus-nanopolish.sh#L99

[Merritt-Brian]

Basestack (App) assumes sequencing_summary file is in the base run directory. Recursive checking can be performed from the UI to see if it is present anywhere. But duplicate .txt files will always break the pipeline at module 4