Merge a13b200 into f5078cb

broadinstitute · Apr 10, 2019 · 156deb6 · 156deb6
2 parents f5078cb + a13b200
commit 156deb6
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/pipes/WDL/workflows/tasks/tasks_reports.wdl b/pipes/WDL/workflows/tasks/tasks_reports.wdl
@@ -161,6 +161,7 @@ task spikein_report {
   File  reads_bam
   File  spikein_db
   Int?  minScoreToFilter = 60
+  Int?  topNHits = 3
 
   String reads_basename=basename(reads_bam, ".bam")
 
@@ -171,13 +172,17 @@ task spikein_report {
     read_utils.py bwamem_idxstats \
       ${reads_basename}.bam \
       ${spikein_db} \
-      --outStats ${reads_basename}.spike_count.txt \
+      --outStats ${reads_basename}.spike_count.txt.unsorted \
       --minScoreToFilter=${minScoreToFilter} \
       --loglevel=DEBUG
+
+      sort -b -r -n -k3 ${reads_basename}.spike_count.txt.unsorted > ${reads_basename}.spike_count.txt
+      head -n ${topNHits} ${reads_basename}.spike_count.txt > ${reads_basename}.spike_count.top_${topNHits}_hits.txt
   }
 
   output {
     File   report           = "${reads_basename}.spike_count.txt"
+    File   report_top_hits  = "${reads_basename}.spike_count.top_${topNHits}_hits.txt"
     String viralngs_version = "viral-ngs_version_unknown"
   }
 

diff --git a/pipes/rules/reports.rules b/pipes/rules/reports.rules
@@ -97,7 +97,8 @@ if config.get("spikeins_db"):
             input_bam   = config["data_dir"]+'/'+config["subdirs"]["depletion"]+'/{sample}.cleaned.bam',
             spikeins_db = objectify_remote(config["spikeins_db"])
         output: 
-            config["reports_dir"]+'/spike_count/{sample}.spike_count.txt'
+            config["reports_dir"]+'/spike_count/{sample}.spike_count.txt',
+            config["reports_dir"]+'/spike_count/{sample}.spike_count_top_3.txt'
         resources: 
             mem_mb = 3*1000
         params: 
@@ -107,7 +108,10 @@ 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} --minScoreToFilter 60")
+            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:
         input: