2) Config file

To run filotools is necessary to set up a tab separated file named "default.config" containing the path of key elements for the analysis. The file must be stored in ./filotools/config_files

the mandatory fields are

fastq_path
bam_path
reference
chr_list

All the other fields can be left as "default" and the program will automatically create the paths for the analysis. A user that wants to redirect filotools input/outputs can specify the other fields, but "force config" should be used when launching commands.

an example of config file:

fastq_path	/path/to/demultiplexed_fastqs
bam_path	/path/to/aligned_bams
reference	/path/to/reference/GCF_000001405.39_GRCh38.p13_genomic.fna
stats_path	default
motif_path	default
motif_count_path	default
readl_path	default
raw_readl_path	default
chr_list	/path/to/filotools/utility/chr_list.txt
basecall_path	default
barcoding_path	default
merged_fastq_path	default