sort by names

alsmith151 · Jun 28, 2024 · 9dedba7 · 9dedba7
1 parent 356479b
commit 9dedba7
Showing 1 changed file with 2 additions and 5 deletions.
diff --git a/seqnado/workflow/rules/pileup_default.smk b/seqnado/workflow/rules/pileup_default.smk
@@ -133,17 +133,14 @@ rule fragment_bedgraph:
         "seqnado_output/logs/bedgraphs/{sample}.log",
     shell:
         """
-        samtools sort -@ {threads} -o {params.outdir}/{wildcards.sample}_sorted.bam {input.bam} -T {params.outdir}/tmp_{wildcards.sample} 2> {log}
-        samtools index {params.outdir}/{wildcards.sample}_sorted.bam 2>> {log}
+        samtools sort -n -@ {threads} -o {params.outdir}/{wildcards.sample}_sorted.bam {input.bam} -T {params.outdir}/tmp_{wildcards.sample} 2> {log}
         bedtools bamtobed -bedpe -i {params.outdir}/{wildcards.sample}_sorted.bam > {params.outdir}/{wildcards.sample}.bedpe 2>> {log}
         awk '$1 == $4 && $6 - $2 < 1000 {{print $1, $2, $6}}' {params.outdir}/{wildcards.sample}.bedpe > {params.outdir}/{wildcards.sample}_filtered.bed 2>> {log}
         sort -k1,1 -k2,2n -k3,3n {params.outdir}/{wildcards.sample}_filtered.bed > {params.outdir}/{wildcards.sample}_sorted.bed 2>> {log}
-        bedtools genomecov -bg -i {params.outdir}/{wildcards.sample}_sorted.bed -g {params.genome} -threads {threads} > {output.bedgraph} 2>> {log}
-        
+        bedtools genomecov -bg -i {params.outdir}/{wildcards.sample}_sorted.bed -g {params.genome} > {output.bedgraph} 2>> {log}
         rm {params.outdir}/{wildcards.sample}.bedpe
         rm {params.outdir}/{wildcards.sample}_filtered.bed
         rm {params.outdir}/{wildcards.sample}_sorted.bed
         rm {params.outdir}/{wildcards.sample}_sorted.bam
-        rm {params.outdir}/{wildcards.sample}_sorted.bam.bai
         rm {params.outdir}/tmp*
         """