diff --git a/workflow/rules/assignment.smk b/workflow/rules/assignment.smk index 1d9e783..838f1da 100644 --- a/workflow/rules/assignment.smk +++ b/workflow/rules/assignment.smk @@ -191,7 +191,7 @@ rule assignment_collectBCs: output: "results/assignment/{assignment}/barcodes_incl_other.sorted.tsv.gz", params: - batch_size=getSplitNumber(), + batch_size="--batch-size=%d" % getSplitNumber() if getSplitNumber() > 1 else "", conda: "../envs/default.yaml" log: @@ -199,7 +199,7 @@ rule assignment_collectBCs: shell: """ export LC_ALL=C # speed up sort - sort -S 7G --batch-size={params.batch_size} --parallel={threads} -k1,1 -k2,2 -k3,3 -m {input} | \ + sort -S 7G {params.batch_size} --parallel={threads} -k1,1 -k2,2 -k3,3 -m {input} | \ gzip -c > {output} 2> {log} """