conda activate --stack

count.smk

@@ -22,7 +22,6 @@ rule mapping:
 		R2 = "DATA/trim/{reads}_R2.fastq.gz",
 		i = expand("work/index/{{sample}}.{ext}.bt2l", ext=["1", "2", "3", "4", "rev.1", "rev.2"])
 	output:
-		sam = temp("work/bowtie/align-{sample}-{reads}.sam"),
 		bam = "work/bowtie/align-{sample}-{reads}.bam",
 		bai = "work/bowtie/align-{sample}-{reads}.bam.bai"
 	params:
@@ -32,22 +31,19 @@ rule mapping:
 	shell:
 		"conda activate bowtie2-2.4.1 "
 		"&& "
+		"conda activate --stack samtools-1.9 "		
+		"&& "
 		"bowtie2 "
 		"--threads {threads} "
 		"-x {params.index} "
 		"-1 {input.R1} "
 		"-2 {input.R2} "
-		"-S {output.sam} "
-		"&& "
-		"conda deactivate "
-		"&& "
-		"conda activate samtools-1.9 "
-		"&& "
+		"-S - "
+		"| "
 		"samtools view "
 		"--threads {threads} "
 		"-b "
 		"-o {output.bam} "
-		"{output.sam} "
 		"&& "
 		"samtools sort "
 		"--threads {threads} "