increase resources for fragment

alsmith151 · Jul 6, 2024 · 28df5a8 · 28df5a8
1 parent 45982ae
commit 28df5a8
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Showing 2 changed files with 2 additions and 461 deletions.
diff --git a/seqnado/workflow/rules/pileup_default.smk b/seqnado/workflow/rules/pileup_default.smk
@@ -127,7 +127,7 @@ rule fragment_bedgraph:
         genome=config["genome"]["chromosome_sizes"]
     threads: config["deeptools"]["threads"],
     resources:
-        runtime=lambda wildcards, attempt: f"{4 * 2 ** (attempt - 1)}h",
+        runtime="4h",
         mem=lambda wildcards, attempt: f"{4 * 2 ** (attempt - 1)}GB",
     log:
         "seqnado_output/logs/bedgraphs/{sample}.log",
@@ -138,7 +138,7 @@ rule fragment_bedgraph:
         bedtools bamtobed -bedpe -i {params.outdir}/{wildcards.sample}_sorted_name.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