From 17cdbd13a8ea3288eb0e334cbb81a694f64b659e Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 18 May 2020 13:30:15 +0200
Subject: [PATCH] make pdf files optional
---
picard.wdl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/picard.wdl b/picard.wdl
index 5393cd3..e927550 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -114,7 +114,7 @@ task CollectMultipleMetrics {
File baitBiasDetail = basename + ".bait_bias_detail_metrics"
File baitBiasSummary = basename + ".bait_bias_summary_metrics"
File baseDistributionByCycle = basename + ".base_distribution_by_cycle_metrics"
- File baseDistributionByCyclePdf = basename + ".base_distribution_by_cycle.pdf"
+ File? baseDistributionByCyclePdf = basename + ".base_distribution_by_cycle.pdf"
File errorSummary = basename + ".error_summary_metrics"
File gcBiasDetail = basename + ".gc_bias.detail_metrics"
File gcBiasPdf = basename + ".gc_bias.pdf"
@@ -124,9 +124,9 @@ task CollectMultipleMetrics {
File preAdapterDetail = basename + ".pre_adapter_detail_metrics"
File preAdapterSummary = basename + ".pre_adapter_summary_metrics"
File qualityByCycle = basename + ".quality_by_cycle_metrics"
- File qualityByCyclePdf = basename + ".quality_by_cycle.pdf"
+ File? qualityByCyclePdf = basename + ".quality_by_cycle.pdf"
File qualityDistribution = basename + ".quality_distribution_metrics"
- File qualityDistributionPdf = basename + ".quality_distribution.pdf"
+ File? qualityDistributionPdf = basename + ".quality_distribution.pdf"
File qualityYield = basename + ".quality_yield_metrics"
# Using a glob is easier. But will lead to very ugly output directories.
Array[File] allStats = select_all([
--
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