add paired ends and prefetch rule

config.json

 {
-	"THREADS": 8,
-	"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"},
+	"THREADS": 1,
+	"srr": ["SRR1187735"],
+	"SAMPLES": ["SRR1187735"],
+	"FIVE_PRIMER": {"SRR1187735": "GTGYCAGCMGCCGCGGTA"},
+	"THREE_PRIMER": {"SRR1187735": "ACTYAAAKGAATTGRCGGGG"},
 	"DATABASE": "/db/frogs_databanks/assignation/16S/silva_132_16S_pintail100/silva_132_16S_pintail100.fasta"
 }

dada2.R

 library(dada2)
 
-derep <- derepFastq(snakemake@input[[1]], verbose = TRUE)
-err <- learnErrors(snakemake@input[[1]], multithread = snakemake@threads, verbose = TRUE)
-dada <- dada(derep, err = err, multithread = snakemake@threads, verbose = TRUE)
+derepF <- derepFastq(snakemake@input[[1]], verbose = TRUE)
+derepR <- derepFastq(snakemake@input[[2]], verbose = TRUE)
+errF <- learnErrors(snakemake@input[[1]], multithread = snakemake@threads, verbose = TRUE)
+errR <- learnErrors(snakemake@input[[2]], multithread = snakemake@threads, verbose = TRUE)
+dadaFs <- dada(derep, err = errF, multithread = snakemake@threads, verbose = TRUE)
+dadaRs <- dada(derep, err = errR, multithread = snakemake@threads, verbose = TRUE)
+mergers <- mergePairs(dadaFs, dadaRs, verbose=TRUE)
 saveRDS(dada, snakemake@output[[1]])

dada2.smk

 rule dada2:
 	input:
-		"work/filter/{sample}.fastq.gz"
+		filt = "work/filter/{sample}_1.fastq.gz"
+		filtrev = "work/filter/{sample}_2.fastq.gz"
 	output:
 		"work/dada/{sample}.rds"
 	threads:

filterAndTrim.R

 library(dada2)
 
-filterAndTrim(snakemake@input[[1]], snakemake@output[[1]], maxN=0, rm.phix=TRUE, compress=TRUE, verbose = TRUE)
+filterAndTrim(snakemake@input[[1]],snakemake@input[[2]] snakemake@output[[1]], maxN=0, rm.phix=TRUE, compress=TRUE, verbose = TRUE)

global.smk

@@ -19,6 +19,7 @@ rule all:
 		"report/abundance.tsv",
 		# "report/tree.nwk"
 
+include: "prefetech.smk"
 include: "quality.smk"
 include: "preprocess.smk"
 include: "dada2.smk"

prefetech.smk

+rule prefetch:
+    output:
+        "DATA/.prefetch/{srr}.sra"
+    params:
+        "{srr} --max-size 50GB -O DATA"
+    log:
+        "DATA/.prefetch/sra/{srr}.log"
+    shell:
+		"conda activate sra-tools-2.10.1 "
+		"&& "
+        "prefetch {params} > {log} 2>&1 && touch {output} "
+		"&& "
+		"conda deactivate "
+ 
+rule fastqdump:
+    input:
+        "DATA/.prefetch/{srr}.sra"
+    output:
+        touch("DATA/done__{srr}_dump")
+    params:
+        args = "-S -O DATA/ -t DATA/",
+        id_srr = "{srr}"
+    log:
+        "DATA/{srr}.log"
+    shell:
+		"conda activate sra-tools-2.10.1 "
+		"&& "
+        "fasterq-dump {params.args} {params.id_srr} > {log} 2>&1 "
+		"&& "
+		"conda deactivate "
\ No newline at end of file

preprocess.smk

 rule cutadapt:
 	input:
-		"DATA/{sample}.fastq.gz"
+		fwd = "DATA/{sample}_1.fastq.gz"
+		rev = "DATA/{sample}_2.fastq.gz"
 	output:
-		"work/cutadapt/{sample}.fastq.gz"
+		cut = "work/cutadapt/{sample}_1.fastq.gz"
+		cutrev = "work/cutadapt/{sample}_2.fastq.gz"
+
 	params:
 		five = lambda wildcards: config["FIVE_PRIMER"][wildcards.sample],
 		three = lambda wildcards: config["THREE_PRIMER"][wildcards.sample]
@@ -22,8 +25,10 @@ rule cutadapt:
 
 rule filter:
 	input:
-		"work/cutadapt/{sample}.fastq.gz"
+		cut = "work/cutadapt/{sample}_1.fastq.gz"
+		cutrev = "work/cutadapt/{sample}_2.fastq.gz"
 	output:
-		"work/filter/{sample}.fastq.gz"
+		filt = "work/filter/{sample}_1.fastq.gz"
+		filtrev = "work/filter/{sample}_2.fastq.gz"
 	script:
 		"filterAndTrim.R"