file-fastq causes validation script to fail

[jmlivingstone]

Using mode 'file-fastq' causes failure but using 'file-fastqfile-bed' is fine. I think line 59-60 in validate_io.py is just missing a comma.

Error executing process > 'run_validate (4)'

Caused by:
Process run_validate (4) terminated with an error exit status (2)

Command executed:

set -euo pipefail
python3 -m validate -t file-fastq CPCG0196-F1-A-mini-0.R2.fq.gz > 'input_validation.txt'

Command exit status:
2

Command output:
(empty)

Command error:
usage: main.py [-h] -t
{file-input,file-bam,file-vcf,file-fasta,file-fastqfile-bed,file-py,directory-rw,directory-r,md5-gen,sha512-gen}
path
main.py: error: argument -t/--type: invalid choice: 'file-fastq' (choose from 'file-input', 'file-bam', 'file-vcf', 'file-fasta', 'file-fas
tqfile-bed', 'file-py', 'directory-rw', 'directory-r', 'md5-gen', 'sha512-gen')

Work dir:
/scratch/align-RNA/work/59/e29b88b2f53a9c4b297d18eb0fccb9

[ginakkiim]

working on this issue!