Commit b852f88e authored by Cedric Midoux's avatar Cedric Midoux
Browse files

hotfix2021

parent a5c717b9
......@@ -3,7 +3,7 @@
{
"out" : "LOGS/",
"err" : "LOGS/",
"queue" : "short.q,long.q,maiage.q",
"queue" : "short.q@@recentNodes",
"cluster" : ""
}
}
......@@ -3,5 +3,5 @@
"SAMPLES": ["4A", "5A", "6A", "7A", "8A", "9A", "10A", "11A", "12A"],
"FIVE_PRIMER": {"4A": "GTGYCAGCMGCCGCGGTA", "5A": "GTGYCAGCMGCCGCGGTA","6A": "GTGYCAGCMGCCGCGGTA","7A": "GTGYCAGCMGCCGCGGTA","8A": "GTGYCAGCMGCCGCGGTA","9A": "GTGYCAGCMGCCGCGGTA","10A": "GTGYCAGCMGCCGCGGTA","11A": "GTGYCAGCMGCCGCGGTA","12A": "GTGYCAGCMGCCGCGGTA"},
"THREE_PRIMER": {"4A": "ACTYAAAKGAATTGRCGGGG", "5A": "ACTYAAAKGAATTGRCGGGG","6A": "ACTYAAAKGAATTGRCGGGG","7A": "ACTYAAAKGAATTGRCGGGG","8A": "ACTYAAAKGAATTGRCGGGG","9A": "ACTYAAAKGAATTGRCGGGG","10A": "ACTYAAAKGAATTGRCGGGG","11A": "ACTYAAAKGAATTGRCGGGG","12A": "ACTYAAAKGAATTGRCGGGG"},
"DATABASE": "/db/frogs_databanks/assignation/16S/silva_132_16S_pintail100/silva_132_16S_pintail100.fasta"
"DATABASE": "/db/frogs_databanks/assignation/silva_138_16S_pintail100/silva_138_16S_pintail100.fasta"
}
library(Matrix, lib.loc='/usr/local/public/R-4.0.3/lib64/R/old_library')
library(dada2)
derep <- derepFastq(snakemake@input[[1]], verbose = TRUE)
......
library(Matrix, lib.loc='/usr/local/public/R-4.0.3/lib64/R/old_library')
library(dada2)
filterAndTrim(snakemake@input[[1]], snakemake@output[[1]], maxN=0, rm.phix=TRUE, compress=TRUE, verbose = TRUE)
library(Matrix, lib.loc='/usr/local/public/R-4.0.3/lib64/R/old_library')
library(dada2)
library(biomformat)
......
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