From 57b803ed917d98bd0d187bdffe1d7995fa1c770a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas=20FERNANDEZ=20NU=C3=91EZ?=
<fernandez.nunez.nicolas@gmail.com>
Date: Thu, 7 Oct 2021 12:41:42 +0200
Subject: [PATCH] Same as Sickle, replace fastq-screen --quiet option with
shortcut -q to avoid segmentatin fault 11
---
RQCP.sh | 10 +++++-----
workflow/rules/reads_quality_control_pipeline.smk | 11 ++++++-----
2 files changed, 11 insertions(+), 10 deletions(-)
diff --git a/RQCP.sh b/RQCP.sh
index 3b3e6e0..55164f8 100755
--- a/RQCP.sh
+++ b/RQCP.sh
@@ -53,8 +53,8 @@ snakemake --directory ${WORKDIR} --use-conda --keep-going --rerun-incomplete -s
snakemake --directory ${WORKDIR} --use-conda --keep-going --rerun-incomplete -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --cores # at last, real run
###### Create usefull graphs and summary
-mkdir ${WORKDIR}/results/Graphics/ 2> /dev/null
-snakemake --directory ${WORKDIR} --use-conda -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --dag | dot -Tpdf > ${WORKDIR}/results/Graphics/DAGraph.pdf
-snakemake --directory ${WORKDIR} --use-conda -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --rulegraph | dot -Tpdf > ${WORKDIR}/results/Graphics/RuleGraph.pdf
-snakemake --directory ${WORKDIR} --use-conda -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --filegraph | dot -Tpdf > ${WORKDIR}/results/Graphics/FileGraph.pdf
-snakemake --directory ${WORKDIR} --use-conda -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --summary > ${WORKDIR}/results/Graphics/Summary.txt
+mkdir ${WORKDIR}/results/graphs/ 2> /dev/null
+snakemake --directory ${WORKDIR} --use-conda -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --dag | dot -Tpdf > ${WORKDIR}/results/graphs/DAGraph.pdf
+snakemake --directory ${WORKDIR} --use-conda -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --rulegraph | dot -Tpdf > ${WORKDIR}/results/graphs/RuleGraph.pdf
+snakemake --directory ${WORKDIR} --use-conda -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --filegraph | dot -Tpdf > ${WORKDIR}/results/graphs/FileGraph.pdf
+snakemake --directory ${WORKDIR} --use-conda -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --summary > ${WORKDIR}/results/graphs/Summary.txt
diff --git a/workflow/rules/reads_quality_control_pipeline.smk b/workflow/rules/reads_quality_control_pipeline.smk
index 314d497..559ff1a 100644
--- a/workflow/rules/reads_quality_control_pipeline.smk
+++ b/workflow/rules/reads_quality_control_pipeline.smk
@@ -105,8 +105,8 @@ rule fastqscreen:
"results/reports/fastq-screen/{qcdir}.log"
shell:
"fastq_screen " # FastqScreen, what did you expect ?
- "--quiet " # -q: Only show log warning
- "--threads {resources.cpus} " # -t: Specifies across how many threads bowtie will be allowed to run
+ "-q " # --quiet: Only show log warning
+ "--threads {resources.cpus} " # --threads: Specifies across how many threads bowtie will be allowed to run
"--conf {params.config} " # path to configuration file
"--aligner {params.aligner} " # -a: choose aligner 'bowtie', 'bowtie2', 'bwa'
"--subset {params.subset} " # Don't use the whole sequence file, but create a subset of specified size
@@ -156,7 +156,8 @@ rule fastqjoin:
output:
forward= "results/reads/fastq-join-unique/{sample}_cutadapt_sickle-trim_fastq-join_Unique_R1.fastq.gz",
reverse = "results/reads/fastq-join-unique/{sample}_cutadapt_sickle-trim_fastq-join_Unique_R2.fastq.gz",
- joined = "results/reads/fastq-join/{sample}_cutadapt_sickle-trim_fastq-join_Mate.fastq.gz"
+ joined = "results/reads/fastq-join/{sample}_cutadapt_sickle-trim_fastq-join_Mate.fastq.gz",
+ report = "results/reports/fastq-join/{sample}_stich_length_report.txt"
log:
"results/reports/fastq-join/{sample}.log"
shell:
@@ -168,8 +169,8 @@ rule fastqjoin:
"-o {output.forward} " # for unique forward files
"-o {output.reverse} " # for unique reverse files
"-o {output.joined} " # for join files
- "-r {log} " # Verbose stitch length report
- #"&> {log}" # Add redirection for log
+ "-r {output.report} " # Verbose stitch length report
+ "&> {log}" # Add redirection for log
###############################################################################
rule sickletrim:
--
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