use absolute path to avoid error with AlienTrimmer

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. 
+# 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
 #===============================================================================