From 5db09352abdcb2af41ae5b72250b26c547951877 Mon Sep 17 00:00:00 2001
From: Thomas Battenfeld <46334240+thomasbtf@users.noreply.github.com>
Date: Wed, 16 Feb 2022 08:05:01 +0100
Subject: [PATCH] fix: canu and porechop logging

---
 workflow/rules/long_read.smk | 35 ++++++++++++++++-------------------
 1 file changed, 16 insertions(+), 19 deletions(-)

diff --git a/workflow/rules/long_read.smk b/workflow/rules/long_read.smk
index d4d70afa6..d356d8053 100644
--- a/workflow/rules/long_read.smk
+++ b/workflow/rules/long_read.smk
@@ -80,7 +80,7 @@ rule porechop_primer_trimming:
         "logs/{date}/trimmed/porechop/primer_clipped/{sample}.log",
     threads: 2
     shell:
-        "(porechop -i {input.fastq_in} -o {output} --no_split --end_size 35 --extra_end_trim 0 -t {threads} -v 1) 2> {log}"
+        "(porechop -i {input.fastq_in} -o {output} --no_split --end_size 35 --extra_end_trim 0 -t {threads} -v 1) > {log} 2>&1"
 
 
 rule nanofilt:
@@ -117,24 +117,21 @@ 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}
-        )
-        2> {log}
-        """
+        "( 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: