From 78fb9b3ecb37cd0f655cb7bf0b6bc15d4ac08d13 Mon Sep 17 00:00:00 2001 From: MihaelaZavolan <mihaela.zavolan@unibas.ch> Date: Thu, 28 Jul 2022 12:28:10 +0000 Subject: [PATCH] docs: add/extend input hints --- RUNS/JOB/prepare/config.yaml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/RUNS/JOB/prepare/config.yaml b/RUNS/JOB/prepare/config.yaml index 3e1a5bb..cb04adf 100644 --- a/RUNS/JOB/prepare/config.yaml +++ b/RUNS/JOB/prepare/config.yaml @@ -15,18 +15,25 @@ bp_3p: [0] # array of numbers, e.g., [-2,-1,0,+1], to include 2 upstream and 1 d # 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"; names have to match precisely +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 -- GitLab