Evert.van schaik master patch 73418

FROGS

+###FROGS for 16S
+### CHECK PARAMETERS 
+conda activate frogs-3.2.2
+preprocess.py illumina --input-archive ffiles.tar.gz --min-amplicon-size 200 --max-amplicon-size 700 --merge-software flash --five-prim-primer CCTACGGGAGGCAGCAG --three-prim-primer ATTAGAWACCCVHGTAGTCC --R1-size 300 --R2-size 300 --nb-cpus 8 --output-dereplicated FROGS/preprocess2.fasta --output-count FROGS/preprocess2.tsv --summary FROGS/preprocess2.html --log-file FROGS/preprocess2.log
+
+clustering.py --input-fasta FROGS/preprocess.fasta --input-count FROGS/preprocess.tsv --distance 1 --fastidious --nb-cpus 8 --log-file FROGS/clustering.log --output-biom FROGS/clustering.biom --output-fasta FROGS/clustering.fasta --output-compo FROGS/clustering_otu_compositions.tsv
+
+remove_chimera.py --input-fasta FROGS/clustering.fasta --input-biom FROGS/clustering.biom --non-chimera FROGS/remove_chimera.fasta --nb-cpus 8 --log-file FROGS/remove_chimera.log --out-abundance FROGS/remove_chimera.biom --summary FROGS/remove_chimera.html
+
+otu_filters.py --input-fasta FROGS/remove_chimera.fasta --input-biom FROGS/remove_chimera.biom --output-fasta FROGS/filters.fasta --nb-cpus 8 --log-file FROGS/filters.log --output-biom FROGS/filters.biom --summary FROGS/filters.html --excluded FROGS/filters_excluded.tsv --contaminant /db/frogs_databanks/contaminants/phi.fa --min-sample-presence 1 --min-abundance 0.00005
+
+affiliation_OTU.py --input-fasta FROGS/filters.fasta --input-biom FROGS/filters.biom --nb-cpus 8 --log-file FROGS/affiliation.log --output-biom FROGS/affiliation.biom --summary FROGS/affiliation.html --reference /db/frogs_databanks/assignation/silva_138_16S/silva_138_16S.fasta
+
+biom_to_tsv.py --input-biom FROGS/affiliation.biom --input-fasta FROGS/filters.fasta --output-tsv FROGS/affiliation.tsv --output-multi-affi FROGS/multi_aff.tsv --log-file FROGS/biom_to_tsv.log  
+conda deactivate