diff --git a/config/config.yaml b/config/config.yaml index d3e76ee14c92ffe616571a714a73948342eb4100..6140d4988596a6c2293e96a623ca610817fc7a2a 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -25,32 +25,35 @@ # Config file for RNAflow pipeline #========================================================= -# directory where fastq are stored -input_dir: ../data +# Absolute path of directory where fastq are stored +input_dir: /absolute/path/to/data # How mate paires are written in fastq input_mate: '_R[12]' # filemame extension input_extension: '.fastq.gz' -# directory where you want +# directory where you want (not yet fonctional sorry) analysis_dir: . # tmpdir: write tempory file on this directory (default /tmp/, but could be "/pasteur/sonic/scratch/users/LOGIN/") tmpdir: "/pasteur/sonic/scratch/public/" #=============================================================================== -# Indexing section: if checked, indexes for bowtie2 mapping will be produced in -# genome_directory +# Genome Section +# Note that this pipeline is conceived to used one or more genome. +#Â Please always fill the four first lines. # # :Parameters: # -# - index: assuming needed indexes are here if False # - genome_directory: directory where all indexed are written -# - name: name of prefix use in all output files from mapping -# - fasta_file: path to Reference Genome in fasta format -# - host_mapping: set to True if you want align reads also against another genome -# - host_name: name of prefix use in all output files from mapping related to host -# - host_fasta_file: path related to another genome in fasta format -# - rRNA_mapping: Mapping on ribosomal RNA +# - name: name of prefix use in all output files from mapping [First Genome] +# - fasta_file: path to Reference Genome in fasta format [First Genome] +# - gff_file : path to annotation file [First Genome] +# - host_mapping: set to True if you want align reads also against another genome [Second Genome] +# - host_name: name of prefix use in all output files from mapping related to [Second Genome] +# - host_fasta_file: path related to another genome in fasta format [Second Genome] +# - gff_file : path to annotation file [Second Genome] +# - rRNA_mapping: Mapping on ribosomal RNA. If true, sortmeRNA is used to estimate ribosomal rate +# - ribo_fasta_file : path to ribosomal sequences in fasta format #===============================================================================