config.yml

### General Params
verbose: TRUE
threads: 12
memory: 12G
overwrite_results: FALSE
clean_tmp_files: TRUE
remove_clipped_bam: FALSE
plot_format: "pdf"

### in/out paths
input_path: "./input/"
results_path: "./results/"
#anaconda_bin_path: "/opt/anaconda/bin/"

### Reference Data - Path
ref_data_path: "./referenceData/"
### Reference Data - Files
#ref_data_sequence_file: "hg38.fa"
#ref_data_intervals_file: "SeqCap_EPI_CpGiant_hg38_custom_liftOver.bed"
ref_data_sequence_file: "hg38_NC_001416.fa"
ref_data_intervals_file: "SeqCap_EPI_CpGiant_hg38_custom_liftOver_NC_001416.bed"
ref_control_sequence_name: "NC_001416"

### Reference Data - Remaining Files
ref_data_trimmomatic_adapter: "Trimmomatic/adapters/TruSeq3-PE-2.fa"
ref_data_CpgIslandAnnotation: "cpgIslandExt.hg38.bed"
ref_data_CpGGenomAnnotation: "geneAnnotationEnsemble.hg38.bed"

### Specific Tools params
trimmomatic_MINLEN: 50
sqtk_run: FALSE
sqtk_subset: 10000000
min_depth: 1
#meth_tool: ['methratio', 'bssnper']
meth_tool:  ['methratio','bssnper']
#meth_processing: ["allCHR","batchCHR"]
meth_processing: "batchCHR"