diff --git a/Snakefile b/Snakefile index 4e6ef9b30..d74e95449 100755 --- a/Snakefile +++ b/Snakefile @@ -498,7 +498,7 @@ rule bigwig: "envs/environment.yaml" shell: "echo 'bedtools version:\n' > {log}; bedtools --version >> {log}; " - "bedtools genomecov -split -ibam {input.bam} -bg | sort -k1,1 -k2,2n > " + "bedtools genomecov -split -ibam {input.bam} -bg | LC_COLLATE=C sort -k1,1 -k2,2n > " "{params.STARbigwigdir}/{wildcards.sample}_Aligned.sortedByCoord.out.bedGraph; " "bedGraphToBigWig {params.STARbigwigdir}/{wildcards.sample}_Aligned.sortedByCoord.out.bedGraph " "{input.chrl} {output}; rm -f {params.STARbigwigdir}/{wildcards.sample}_Aligned.sortedByCoord.out.bedGraph"