Add new file

Integron_Prediction/Snakefile

+# Predict Integrons
+
+configfile: "config.yaml"
+
+rule all:
+        input: expand(["{datadir}/{project}/{sample}.attc.adj.txt", "{datadir}/{project}/{sample}.intI.txt","{datadir}/{project}/{sample}_integron_prediction.tsv"], datadir=config["integrons"]["datadir"], project=config["integrons"]["project"], sample=config["integrons"]["sample"])
+
+
+rule attC:
+        input: "{datadir}/{sample}.fna"
+        output: "{datadir}/{project}/{sample}.attc.txt", "{datadir}/{project}/{sample}.attc.adj.txt"
+        shell: """
+                export PATH={config[integrons][HattCI]}:$PATH
+                hattci.out {input} {output[0]}
+                sed -i -n '/--------------------------------------------/q;p' {output[0]}
+                cut -f 2,5 -d$'\t' {output[0]} > {output[1]}
+                """
+
+rule intI:
+        input: "{datadir}/{sample}.fna"
+        output: "{datadir}/{project}/{sample}.intI.txt"
+        conda: "hmm.yaml"
+        shell: "nhmmscan --noali --notextw --tblout {output} hmm_model_integron/intI.hmm {input}"
+
+rule Integrons:
+        input:
+                attc="{datadir}/{project}/{sample}.attc.adj.txt",
+                intI="{datadir}/{project}/{sample}.intI.txt"
+        output: Integrons="{datadir}/{project}/{sample}_integron_prediction.tsv"
+        conda: "R.yaml"
+        script: "Integron.R"
+        
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