Commit 184bad7b authored by Cedric Midoux's avatar Cedric Midoux
Browse files

conda activate --stack

parent 6c0ba280
......@@ -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} "
......
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