chore: remove unused config file

workflow/config.yaml

----
-#### GLOBAL PARAMETERS #####
-
-# Directories
-# Usually there is no need to change these
-map_input_dir: "path/to/map_input_directory" # For the mapping worflow
-quantify_input_dir: "path/to/quantify_input_directory" # For the quantify worflow
-output_dir: "results"
-scripts_dir: "../scripts"
-local_log: "logs/local"
-cluster_log: "logs/cluster"
-
-# Inputs information
-sample: ["sample_1", "sample_2"]  # put all sample names, separated by comma
-
-#######################################################################################################
-####
-#### PREPARE PARAMETERS
-####
-#######################################################################################################
-
-# Isomirs annotation file
-# Number of base pairs to add/substract from 5' (start) and 3' (end) coordinates.
-bp_5p: [0] # array of numbers, e.g., [-2,-1,0,+1], to include 2 upstream and 1 downstream nts
-bp_3p: [0] # array of numbers, e.g., [-2,-1,0,+1], to include 2 upstream and 1 downstream nts
-
-# List of inputs
-organism: ["org/pre"] # e.g., ["homo_sapiens/GRCh38.100", "mus_musculus/GRCm37.98"]
-# this string specifies a path, and the "/" is important for this
-# "pre" specifies the assembly version
-
-
-#### PARAMETERS SPECIFIC TO INPUTS #####
-
-org/pre: # One section for each list item in "organism"; entry should match precisely what
-# is in the "organism" section above, one entry per list item above, omitting the ""
-  # URLs to genome, gene & miRNA annotations
-  genome_url: # FTP/HTTP URL to gzipped genome in FASTA format, Ensembl style
-  # e.g. "ftp://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz"
-  gtf_url: # FTP/HTTP URL to gzipped gene annotations in GTF format, Ensembl style
-  # e.g. "ftp://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.chr.gtf.gz"
-  mirna_url: # FTP/HTTP URL to unzipped microRNA annotations in GFF format, miRBase style
-  # e.g. "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
-
-  # Chromosome name mappings between UCSC <-> Ensembl
-  # Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
-  map_chr_url: # FTP/HTTP URL to mapping table
-  # e.g. "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
-  # Chromosome name mapping parameters:
-  column: 1 # Column number from input file where to change chromosome name
-  delimiter: "TAB" # Delimiter of the input file
-
-#######################################################################################################
-####
-#### MAP PARAMETERS
-####
-#######################################################################################################
-
-# Resources: genome, transcriptome, genes, miRs
-# All of these are produced by the "prepare" workflow
-genome: "path/to/genome.processed.fa"
-gtf: "path/to/gene_annotations.filtered.gtf"
-transcriptome: "path/to/transcriptome_idtrim.fa"
-transcriptome_index_segemehl: "path/to/transcriptome_index_segemehl.idx"
-genome_index_segemehl: "path/to/genome_index_segemehl.idx"
-exons: "path/to/exons.bed"
-header_of_collapsed_fasta: "path/to/headerOfCollapsedFasta.sam"
-
-# Tool parameters: quality filter
-q_value: 10  # Q (Phred) score; minimum quality score to keep
-p_value: 50  # minimum % of bases that must have Q quality
-
-# Tool parameters: adapter removal
-error_rate: 0.1  # fraction of allowed errors
-minimum_length: 15  # discard processed reads shorter than the indicated length
-overlap: 3  # minimum overlap length of adapter and read to trim the bases
-max_n: 0  # discard reads containing more than the indicated number of N bases
-
-# Tool parameters: mapping
-max_length_reads: 30  # maximum length of processed reads to map with oligomap
-nh: 100  # discard reads with more mappings than the indicated number
-
-
-#### PARAMETERS SPECIFIC TO INPUTS ####
-
-sample_1:  # one section per list item in "sample"; names have to match
-    adapter: "XXXXXXXXXXXXXXXXXXXX"  # 3' adapter sequence to trim
-    format: "fa"  # file format; currently supported: "fa"
-
-
-#######################################################################################################
-####
-#### QUANTIFY PARAMETERS
-####
-#######################################################################################################
-
-
-# Types of miRNAs to quantify
-# Remove miRNA types you are not interested in
-mir_list: ["miRNA", "miRNA_primary_transcript", "isomirs"]
-
-# Resources: miR annotations, chromosome name mappings
-# All of these are produced by the "prepare" workflow
-mirnas_anno: "path/to/mirna_filtered.bed"
-isomirs_anno: "path/to/isomirs_annotation.bed"
-...
\ No newline at end of file