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# File format #
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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 :
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<sample_name>(. | _)(r1 | R1 | r2 | R2)(fastq | fq | fastq.gz | fq.gz)
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exemple :
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S1.R1.fastq
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S1.R2.fastq
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S2_r1.fq
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S2_r2.fq
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*NOTE* : for now, fastq files must be uncompressed - I'm actually adding a rule for temporary decompressed files.
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# Installation #
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git clone git@gitlab.univ-nantes.fr:bird_pipeline_registry/genosysmics.git
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