From 102bff10bd1ee00a10f7dde24896bb1e731bcbd4 Mon Sep 17 00:00:00 2001
From: jboom1 <j.boom.me@lumc.nl>
Date: Fri, 6 Sep 2019 10:48:52 +0200
Subject: [PATCH] Fixed indentation in command sections
---
minimap2.wdl | 42 +++++++++++++++++++++---------------------
1 file changed, 21 insertions(+), 21 deletions(-)
diff --git a/minimap2.wdl b/minimap2.wdl
index 2166f4d..f01c01b 100644
--- a/minimap2.wdl
+++ b/minimap2.wdl
@@ -39,13 +39,13 @@ task Indexing {
set -e pipefail
mkdir -p $(dirname ~{outputPrefix})
minimap2 \
- ~{true="-H" false="" useHomopolymerCompressedKmer} \
- ~{"-k " + kmerSize} \
- ~{"-w " + minimizerWindowSize} \
- ~{"-I " + splitIndex} \
- ~{"-d " + outputPrefix + ".mmi"} \
- ~{"-t " + cores} \
- ~{referenceFile}
+ ~{true="-H" false="" useHomopolymerCompressedKmer} \
+ ~{"-k " + kmerSize} \
+ ~{"-w " + minimizerWindowSize} \
+ ~{"-I " + splitIndex} \
+ ~{"-d " + outputPrefix + ".mmi"} \
+ ~{"-t " + cores} \
+ ~{referenceFile}
}
output {
@@ -96,20 +96,20 @@ task Mapping {
set -e pipefail
mkdir -p $(dirname ~{outputPrefix})
minimap2 \
- ~{"-x " + presetOption} \
- ~{true="-a" false="" outputSAM} \
- ~{"-G " + maxIntronLength} \
- ~{"-F " + maxFragmentLength} \
- ~{true="-X" false="" skipSelfAndDualMappings} \
- ~{"-N " + retainMaxSecondaryAlignments} \
- ~{"-A " + matchingScore} \
- ~{"-B " + mismatchPenalty} \
- ~{"-u " + howToFindGTAG} \
- ~{true="--secondary=yes" false="--secondary=no" secondaryAlignment} \
- ~{"-o " + outputPrefix} \
- ~{"-t " + cores} \
- ~{referenceFile} \
- ~{queryFile}
+ ~{"-x " + presetOption} \
+ ~{true="-a" false="" outputSAM} \
+ ~{"-G " + maxIntronLength} \
+ ~{"-F " + maxFragmentLength} \
+ ~{true="-X" false="" skipSelfAndDualMappings} \
+ ~{"-N " + retainMaxSecondaryAlignments} \
+ ~{"-A " + matchingScore} \
+ ~{"-B " + mismatchPenalty} \
+ ~{"-u " + howToFindGTAG} \
+ ~{true="--secondary=yes" false="--secondary=no" secondaryAlignment} \
+ ~{"-o " + outputPrefix} \
+ ~{"-t " + cores} \
+ ~{referenceFile} \
+ ~{queryFile}
}
output {
--
GitLab