From a417d49e9cfb26906dc9522363706482e82940f3 Mon Sep 17 00:00:00 2001 From: kevinlibuit Date: Fri, 29 Jan 2021 08:11:25 +0000 Subject: [PATCH] grab appropriate pre-primertrimmed bam for qc metrics --- tasks/task_ont_medaka.wdl | 1 + workflows/wf_clear_labs_viral_pipeline_local.wdl | 2 +- workflows/wf_clearlabs_viral_refbased_assembly.wdl | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/tasks/task_ont_medaka.wdl b/tasks/task_ont_medaka.wdl index a36c525..5eda193 100644 --- 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 index 5488245..2ae7150 100644 --- 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 index bbe45eb..abf400d 100644 --- 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: