new rule gmapIndexTarget to prepare the whole genome index of the target...

new rule gmapIndexTarget to prepare the whole genome index of the target genome. This index is needed to rescue genes without any mapping result in targeted mapping and gmap on target

rules/preprocessGenomes.smk

@@ -8,4 +8,12 @@ rule indexTarget:
 	message: " Indexing Target fasta file using samtools faidx"
 	input: config['targetFasta']
 	output: config['targetFasta']+'.fai'
-	shell: "samtools faidx {input}"
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+	shell: "samtools faidx {input}"
+
+rule gmapIndexTarget:
+	message: " Create Gmap Index for rescue"
+	input: config['targetFasta']
+	output: directory(config['results']+"/target_gmapindex")
+	params: indexname="target_gmapindex", indexPath=config['results']
+	log: config['results']+"/target_gmapindex.log"
+	shell: "gmap_build -D {params.indexPath} -d {params.indexname} {input} &> {log}"
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