From 4b3080c51e63419b98c49b4f0bd1dc6dc1de7e37 Mon Sep 17 00:00:00 2001 From: Iris Mestres Pascual <iris.mestrespascual@unibas.ch> Date: Mon, 20 Feb 2023 16:58:44 +0000 Subject: [PATCH] chore: remove unused config file --- workflow/config.yaml | 106 ------------------------------------------- 1 file changed, 106 deletions(-) delete mode 100644 workflow/config.yaml diff --git a/workflow/config.yaml b/workflow/config.yaml deleted file mode 100644 index 25e52d7..0000000 --- a/workflow/config.yaml +++ /dev/null @@ -1,106 +0,0 @@ ---- -#### 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 -- GitLab