Refactor pileup_default.smk to use sorted BAM file for bedtools conve…

…rsion

seqnado/workflow/rules/pileup_default.smk

@@ -127,14 +127,16 @@ rule fragment_bedgraph:
         "seqnado_output/logs/bedgraphs/{sample}.log",
     shell:
         """
-        bedtools bamtobed -bedpe -i {input.bam} > {params.outdir}/{wildcards.sample}.bed 2> {log}
+        samtools sort -n {input.bam} -o {input.bam}.sorted &&
+        bedtools bamtobed -bedpe -i {input.bam}.sorted > {params.outdir}/{wildcards.sample}.bed 2> {log}
         awk '$1==$4 && $6-$2 < 1000 {{print $0}}' {params.outdir}/{wildcards.sample}.bed > {params.outdir}/{wildcards.sample}_clean.bed 2>> {log}
         cut -f 1,2,6 {params.outdir}/{wildcards.sample}_clean.bed | sort -k1,1 -k2,2n -k3,3n > {params.outdir}/{wildcards.sample}_fragments.bed 2>> {log}
         bedtools genomecov -bg -i {params.outdir}/{wildcards.sample}_fragments.bed -g {params.genome} > {output.bedgraph} 2>> {log}
         
         rm {params.outdir}/{wildcards.sample}.bed
         rm {params.outdir}/{wildcards.sample}_clean.bed
         rm {params.outdir}/{wildcards.sample}_fragments.bed
+        rm {input.bam}.sorted
         """
 
 ruleorder: deeptools_make_bigwigs_rna_plus > deeptools_make_bigwigs_rna_minus > deeptools_make_bigwigs