From 2410d0d5c2415f234739f63bbef913f5f531eab7 Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Wed, 17 Mar 2021 11:02:01 +0100
Subject: [PATCH] update dockerImage and re-introduce samtools indexing
---
umi-tools.wdl | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/umi-tools.wdl b/umi-tools.wdl
index 6b3aa69..a09ca64 100644
--- a/umi-tools.wdl
+++ b/umi-tools.wdl
@@ -31,7 +31,7 @@ task Extract {
Boolean threePrime = false
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 2)
- String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
+ String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:f9d5e41daab14b273ff04f257621890af6f82b93-0"
}
command {
@@ -87,7 +87,7 @@ task Dedup {
String memory = "25G"
Int timeMinutes = 30 + ceil(size(inputBam, "G") * 30)
- String dockerImage = "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
+ String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:f9d5e41daab14b273ff04f257621890af6f82b93-0"
}
String outputBamIndex = sub(outputBamPath, "\.bam$", ".bai")
@@ -102,10 +102,12 @@ task Dedup {
~{"--umi-separator=" + umiSeparator} \
~{true="--paired" false="" paired} \
--temp-dir=~{tmpDir}
+ samtools index ~{outputBamPath} ~{outputBamIndex}
}
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"
@@ -132,6 +134,7 @@ 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."}
--
GitLab