Issue Missing input files for rule align

[msalamon2]

Hello,
I am trying to run varCA on scATAC-seq data and I keep running into this error (output from log file):
snakemake) msalamon@esb2:~/varCA$ ./run.bash &
[1]+ Exit 1 ./run.bash (wd: ~/varCA)
(wd now: /home/Projects/Scharer_sc/LRA.MAPseq/analysis/VarCA/output/out_LRA_ATAC_snps)

Building DAG of jobs...
MissingInputException in line 72 of /home/msalamon/varCA/rules/prepare.smk:
Missing input files for rule align

I installed varCA and snakemake without issues, and followed all the steps to modify the config.yaml. I moved my datasets (BAM files, reference genome files and samples tsv file to a "data" folder within varCA and tried to run it from within varCA. I am also confused because I am providing BAM files and line 72 of /home/msalamon/varCA/rules/prepare.smk refers to read alignment with BWA-MEM. These are the files present in the data folder:

It contains the files after indexing the ref genome with BWA, GATK and samtools as instructed.

I am sending in attachment the config.yaml file and the samples.tsv file
error_varCA.zip

Thank you for your help,
Mathilde Salamon