From 35d0b56753ce68327ef43b6fa2828ff6c1a35fce Mon Sep 17 00:00:00 2001
From: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
Date: Wed, 16 Feb 2022 15:17:35 +0100
Subject: [PATCH] Update long_read.smk

add temp flags for different directories
---
 workflow/rules/long_read.smk | 41 +++++++++++++++++++++---------------
 1 file changed, 24 insertions(+), 17 deletions(-)

diff --git a/workflow/rules/long_read.smk b/workflow/rules/long_read.smk
index d356d8053..e2877196f 100644
--- a/workflow/rules/long_read.smk
+++ b/workflow/rules/long_read.smk
@@ -52,7 +52,7 @@ rule customize_primer_porechop:
     input:
         get_artic_primer,
     output:
-        "results/.indicators/replacement_notice.txt",
+        temp("results/.indicators/replacement_notice.txt"),
     conda:
         "../envs/primechop.yaml"
     log:
@@ -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) > {log} 2>&1"
+        "(porechop -i {input.fastq_in} -o {output} --no_split --end_size 35 --extra_end_trim 0 -t {threads} -v 1) 2> {log}"
 
 
 rule nanofilt:
@@ -104,6 +104,8 @@ rule canu_correct:
         "results/{date}/trimmed/nanofilt/{sample}.fastq",
     output:
         "results/{date}/corrected/{sample}/{sample}.correctedReads.fasta.gz",
+        temp(directory("results/{date}/corrected/{sample}/correction")),
+        temp(directory("results/{date}/corrected/{sample}/{sample}.seqStore")),
     log:
         "logs/{date}/canu/assemble/{sample}.log",
     params:
@@ -113,25 +115,30 @@ rule canu_correct:
         for_testing=lambda w, threads: get_if_testing(
             f"corThreads={threads} redMemory=6 oeaMemory=6"
         ),
+    resources:
+        parallel_correction_processes=1,
     conda:
         "../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: