From 3b5f1476fb34d215d6332b127995ff3ab1b82f20 Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Mon, 8 Mar 2021 11:02:53 +0100
Subject: [PATCH] remove umitools deduped BAM index output
---
umi-tools.wdl | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/umi-tools.wdl b/umi-tools.wdl
index 1a7db32..e909e48 100644
--- a/umi-tools.wdl
+++ b/umi-tools.wdl
@@ -103,13 +103,11 @@ task Dedup {
~{"--output-stats " + statsPrefix} \
~{"--umi-separator=" + umiSeparator} \
~{true="--paired" false="" paired} \
- --temp-dir=~{tmpDir} \
- samtools index ~{outputBamPath} ~{outputBamIndex}
+ --temp-dir=~{tmpDir}
}
output {
File deduppedBam = outputBamPath
- File deduppedBamIndex = outputBamIndex
File? editDistance = "~{statsPrefix}_edit_distance.tsv"
File? umiStats = "~{statsPrefix}_per_umi.tsv"
File? positionStats = "~{statsPrefix}_per_umi_per_position.tsv"
@@ -136,7 +134,6 @@ task Dedup {
# outputs
deduppedBam: {description: "Deduplicated BAM file."}
- deduppedBamIndex: {description: "Index of the deduplicated BAM file."}
editDistance: {description: "Report of the (binned) average edit distance between the UMIs at each position."}
umiStats: {description: "UMI-level summary statistics."}
positionStats: {description: "The counts for unique combinations of UMI and position."}
--
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