From 63ae2468f44ab7a5c1ca1059a91f75344a73e05f Mon Sep 17 00:00:00 2001
From: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
Date: Wed, 16 Feb 2022 15:24:24 +0100
Subject: [PATCH] Update long_read.smk

---
 workflow/rules/long_read.smk | 33 +++++++++++++++------------------
 1 file changed, 15 insertions(+), 18 deletions(-)

diff --git a/workflow/rules/long_read.smk b/workflow/rules/long_read.smk
index 548634cb2..291545a78 100644
--- a/workflow/rules/long_read.smk
+++ b/workflow/rules/long_read.smk
@@ -121,24 +121,21 @@ rule canu_correct:
         "../envs/canu.yaml"
     threads: 16
     shell:
-        """
-        ( if [ -d {params.outdir} ]; then rm -Rf {params.outdir}; fi &&
-        canu -correct -nanopore {input} -p {wildcards.sample} -d {params.outdir} genomeSize=30k minOverlapLength=10 minReadLength=200 \
-        useGrid=false {params.for_testing} \
-        corMMapMerSize=10 corOutCoverage=50000 corMinCoverage=0 maxInputCoverage=20000 \
-        corOverlapper=minimap utgOverlapper=minimap obtOverlapper=minimap \
-        corConcurrency={params.concurrency} \
-        cormhapConcurrency={params.concurrency} cormhapThreads={params.concurrency} \
-        cormmapConcurrency={params.concurrency} cormmapThreads={params.concurrency} \
-        obtmmapConcurrency={params.concurrency} obtmmapThreads={params.concurrency} \
-        utgmmapConcurrency={params.concurrency} utgmmapThreads={params.concurrency} \
-        redConcurrency={params.concurrency} redThreads={params.concurrency} \
-        ovbConcurrency={params.concurrency} \
-        ovsConcurrency={params.concurrency} \
-        oeaConcurrency={params.concurrency}
-        )
-        > {log} 2>&1
-        """
+        "( if [ -d {params.outdir} ]; then rm -Rf {params.outdir}; fi &&"
+        " canu -correct -nanopore {input} -p {wildcards.sample} -d {params.outdir} genomeSize=30k minOverlapLength=10 minReadLength=200"
+        " useGrid=false {params.for_testing}"
+        " corMMapMerSize=10 corOutCoverage=50000 corMinCoverage=0 maxInputCoverage=20000"
+        " corOverlapper=minimap utgOverlapper=minimap obtOverlapper=minimap"
+        " corConcurrency={params.concurrency}"
+        " cormhapConcurrency={params.concurrency} cormhapThreads={params.concurrency}"
+        " cormmapConcurrency={params.concurrency} cormmapThreads={params.concurrency}"
+        " obtmmapConcurrency={params.concurrency} obtmmapThreads={params.concurrency}"
+        " utgmmapConcurrency={params.concurrency} utgmmapThreads={params.concurrency}"
+        " redConcurrency={params.concurrency} redThreads={params.concurrency}"
+        " ovbConcurrency={params.concurrency}"
+        " ovsConcurrency={params.concurrency}"
+        " oeaConcurrency={params.concurrency})"
+        "> {log} 2>&1"
 
 
 # rule medaka_consensus_reference: