grab appropriate pre-primertrimmed bam for qc metrics

AndrewLangvt · Jan 29, 2021 · a417d49 · a417d49
1 parent 931d10d
commit a417d49
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Showing 3 changed files with 3 additions and 2 deletions.
diff --git a/tasks/task_ont_medaka.wdl b/tasks/task_ont_medaka.wdl
@@ -94,6 +94,7 @@ task consensus {
 
   output {
     File    consensus_seq = "${samplename}.consensus.fasta"
+    File    sorted_bam = "${samplename}.trimmed.rg.sorted.bam"
     File    trim_sorted_bam = "${samplename}.primertrimmed.rg.sorted.bam"
     File    trim_sorted_bai = "${samplename}.primertrimmed.rg.sorted.bam.bai"
     Int     number_N = read_string("NUM_N")

diff --git a/workflows/wf_clear_labs_viral_pipeline_local.wdl b/workflows/wf_clear_labs_viral_pipeline_local.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "wf_clear_labs_viral_refbased_assembly.wdl" as assembly
+import "wf_clearlabs_viral_refbased_assembly.wdl" as assembly
 import "../tasks/task_amplicon_metrics.wdl" as assembly_metrics
 import "../tasks/task_clear_labs_sample_metrics.wdl" as summary
 import "wf_ont_sc2_pubRepo_submission.wdl" as submission

diff --git a/workflows/wf_clearlabs_viral_refbased_assembly.wdl b/workflows/wf_clearlabs_viral_refbased_assembly.wdl
@@ -31,7 +31,7 @@ workflow viral_refbased_assembly {
   call assembly_metrics.stats_n_coverage {
     input:
       samplename = samplename,
-      bamfile = consensus.trim_sorted_bam
+      bamfile = consensus.sorted_bam
   }
   call assembly_metrics.stats_n_coverage as stats_n_coverage_primtrim {
     input: