Installation.md

+# File format #
+
+Metagenomics samples must be stored in a unique directory. Because there is a high variability in filename format increasing automated paired-end data recognition, filename are constrained and must respect the following format :
+
+<sample_name>(. | _)(r1 | R1 | r2 | R2)(fastq | fq | fastq.gz | fq.gz)
+
+exemple : 
+    S1.R1.fastq
+    S1.R2.fastq
+    S2_r1.fq
+    S2_r2.fq
+
+*NOTE* : for now, fastq files must be uncompressed - I'm actually adding a rule for temporary decompressed files.
+
 # Installation #
 
     git clone git@gitlab.univ-nantes.fr:bird_pipeline_registry/genosysmics.git