sort main spikein report produced by snakemake spikein_report rule

broadinstitute · Apr 10, 2019 · a13b200 · a13b200
1 parent 6366cf0
commit a13b200
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/pipes/rules/reports.rules b/pipes/rules/reports.rules
@@ -108,9 +108,9 @@ if config.get("spikeins_db"):
         run:
             makedirs(os.path.join(config["reports_dir"], 'spike_count'))
             makedirs(os.path.join(config["tmp_dir"], config["subdirs"]["depletion"]))
-            shell("{config[bin_dir]}/read_utils.py bwamem_idxstats {input.input_bam} {input.spikeins_db} --outStats {output[0]} --minScoreToFilter 60")
-            shell("sort -b -r -n -k3 {output[0]} > {config[tmp_dir]}/{output[0]}.sorted")
-            shell("head -n 3 {config[tmp_dir]}/{output[0]}.sorted > {output[1]}")
+            shell("{config[bin_dir]}/read_utils.py bwamem_idxstats {input.input_bam} {input.spikeins_db} --outStats {config[tmp_dir]}/{output[0]} --minScoreToFilter 60")
+            shell("sort -b -r -n -k3 {config[tmp_dir]}/{output[0]} > {output[0]}")
+            shell("head -n 3 {output[0]} > {output[1]}")
 
 
     rule consolidate_spike_count: