Syntax error loading yaml file

[iwanttoeatyo]

Describe the bug

Hello zUMIs developers, thank you for developing such a great tool, I had a little bug when I was using it, I have smartseq2 data

I was using ’git clone https://github.com/sdparekh/zUMIs.git‘ to download the codebase and then using ’sh zUMIs.sh -c -y smartseq2.yaml‘ to analyze it, and the bug appeared

(zUMIs) cqdgkyb@hpc31:~/software_bioinformatics/zUMIs$ sh zUMIs.sh -c -y smartseq2.yaml
Using miniconda environment for zUMIs!
note: internal executables will be used instead of those specified in the YAML file!
Warning message:
package ‘yaml’ was built under R version 4.4.2
Error: Syntax error loading yaml file
Execution halted
YAML file has an error. Look at the zUMIs_YAMLerror.log or contact developers.

I need your help to fix this bug, thanks!

To Reproduce
YAML file
project: samrt-seq2

sequence_files:
file1:
name: /home/cqdgkyb/daping/fastq/CRR058013_S1_R2_001.fastq.gz
base_definition:
- BC(1-8)
- UMI(9-16)
file2:
name: /home/cqdgkyb/daping/fastq/CRR058013_S1_R1_001.fastq.gz
base_definition:
- cDNA(1-300)

reference:
STAR_index: /home/cqdgkyb/software_bioinformatics/star_index
GTF_file: /home/cqdgkyb/software_bioinformatics/gencode.vM36.annotation.gtf

out_dir: /home/cqdgkyb/daping/output

num_threads: 24
mem_limit: 370

filter_cutoffs:
BC_filter:
num_bases: 1
phred: 20
UMI_filter:
num_bases: 1
phred: 20

barcodes:
barcode_num: ~
barcode_file: ~
automatic: yes
BarcodeBinning: 0
nReadsperCell: 100
demultiplex: yes

counting_opts:
introns: yes
downsampling: '0'
strand: 0
Ham_Dist: 0
velocyto: no
primaryHit: yes
twoPass: no

make_stats: yes
which_Stage: Filtering
samtools_exec: samtools
pigz_exec: pigz
STAR_exec: STAR
Rscript_exec: Rscript
zUMIs_directory: /home/cqdgkyb/software_bioinformatics/zUMIs
read_layout: SE

Screenshots
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Desktop (please complete the following information):

• OS: Ubuntu
• Version: 20.04.6 LTS (Focal Fossa)

Additional context
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