diff --git a/test/config_prepare.yaml b/test/config_prepare.yaml deleted file mode 100644 index a74dba6c1bb82d4f8debb794f02b8dc1ea28e3a4..0000000000000000000000000000000000000000 --- a/test/config_prepare.yaml +++ /dev/null @@ -1,33 +0,0 @@ ---- -#### GLOBAL PARAMETERS ##### - -# Directories -# Usually there is no need to change these -output_dir: "results" -scripts_dir: "../scripts" -local_log: "logs/local" -cluster_log: "logs/cluster" - -# Isomirs annotation file -# Number of base pairs to add/substract from 5' (start) and 3' (end) coordinates. -bp_5p: [-1, 0, +1] -bp_3p: [-1, 0, +1] - -# List of inputs -organism: ["homo_sapiens/chrY"] - -#### PARAMETERS SPECIFIC TO INPUTS ##### - -homo_sapiens/chrY: - # URLs to genome, gene & miRNA annotations - genome_url: "ftp://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz" - gtf_url: "ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/Homo_sapiens.GRCh38.98.gtf.gz" - mirna_url: "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: "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt" - # Chromosome name mapping parameters: - column: 1 - delimiter: "TAB" -...