case_control_gwas option error: Missing input files for rule gwas

[1teaspoon]

An issue when setting gwas = True in config.yaml file:

"
Building DAG of jobs...
MissingInputException in line 606 of /scratch/wangj41/slurm_test/04232024_GwasQcPipeline_test/conda/envs/GwasQcPipeline_04232024/lib/python3.8/site-packages/cgr_gwas_qc/workflow/modules/plink.smk:
Missing input files for rule gwas:
subject_level/gwas.txt
sex_chr_included True
gwas = True
"

[1teaspoon]

The entire log is copied below:

################################################################################

CGR SUBMIT: Starting GWAS QC Workflow

User: wangj41

Version: v1.4.0

Profile: /mnt/nfs/dubbletrubble/scratch/wangj41/slurm_test/04232024_GwasQcPipeline_test/conda/envs/GwasQcPipeline_04232024/lib/python3.8/site-packages/cgr_gwas_qc/cluster_profiles/ccad2

Snakefile: /scratch/wangj41/slurm_test/04232024_GwasQcPipeline_test/conda/envs/GwasQcPipeline_04232024/lib/python3.8/site-packages/cgr_gwas_qc/workflow/Snakefile

Cluster Job ID: 1273228

Start Date: 2024-04-29

Start Time: 09:27:24

################################################################################
Building DAG of jobs...
MissingInputException in line 606 of /scratch/wangj41/slurm_test/04232024_GwasQcPipeline_test/conda/envs/GwasQcPipeline_04232024/lib/python3.8/site-packages/cgr_gwas_qc/workflow/modules/plink.smk:
Missing input files for rule gwas:
subject_level/gwas.txt
sex_chr_included True
gwas = True

################################################################################

CGR SUBMIT: There was a workflow error, check logs and re-run.

Exit Code: 1

End Date: 2024-04-29

End Time: 09:27:34

################################################################################