From e47dca808c0384acf9065cac0ef6dd384111461a 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 11:25:58 +0200
Subject: [PATCH] Change Sickle-trim option for one letter than --word because
issue segmentation fault 11
---
.../rules/reads_quality_control_pipeline.smk | 30 +++++++++----------
1 file changed, 15 insertions(+), 15 deletions(-)
diff --git a/workflow/rules/reads_quality_control_pipeline.smk b/workflow/rules/reads_quality_control_pipeline.smk
index 12d4b6f..9640520 100644
--- a/workflow/rules/reads_quality_control_pipeline.smk
+++ b/workflow/rules/reads_quality_control_pipeline.smk
@@ -5,7 +5,7 @@
# Aim: Reads Quality Control
# Date: 2021.04.30
# Run: snakemake --use-conda -s reads_quality_control_pipeline.smk --cores
-# Latest modification: 2021.10.04
+# Latest modification: 2021.10.07
# Todo: ND
###############################################################################
@@ -168,8 +168,8 @@ 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 {log} " # Verbose stitch length report
+ #"&> {log}" # Add redirection for log
###############################################################################
rule sickletrim:
@@ -194,18 +194,18 @@ rule sickletrim:
log:
"results/reports/sickle-trim/{sample}.log"
shell:
- "sickle " # Sickle, a windowed adaptive trimming tool for FASTQ files using quality
- "{params.command} " # Paired-end or single-end sequence trimming
- "-t {params.encoding} " # --qual-type: Type of quality values, solexa ; illumina ; sanger ; CASAVA, < 1.3 ; 1.3 to 1.7 ; >= 1.8
- "-q {params.quality} " # --qual-threshold: Threshold for trimming based on average quality in a window (default: 20)
- "-l {params.length} " # --length-treshold: Threshold to keep a read based on length after trimming (default: 20)
- "-f {input.forward} " # --pe-file1: Input paired-end forward fastq file
- "-r {input.reverse} " # --pe-file2: Input paired-end reverse fastq file
- "-g " # --gzip-output: Output gzipped files
- "-o {output.forward} " # --output-pe1: Output trimmed forward fastq file
- "-p {output.reverse} " # --output-pe2: Output trimmed reverse fastq file (must use -s option)
- "-s {output.single} " # --output-single: Output trimmed singles fastq file
- "&> {log}" # Add redirection for log
+ "sickle " # Sickle, a windowed adaptive trimming tool for FASTQ files using quality
+ "{params.command} " # Paired-end or single-end sequence trimming
+ "--qual-type {params.encoding} " # -t: Type of quality values, solexa ; illumina ; sanger ; CASAVA, < 1.3 ; 1.3 to 1.7 ; >= 1.8
+ "--qual-threshold {params.quality} " # -q: Threshold for trimming based on average quality in a window (default: 20)
+ "--length-treshold {params.length} " # -l: Threshold to keep a read based on length after trimming (default: 20)
+ "--pe-file1 {input.forward} " # -f: Input paired-end forward fastq file
+ "--pe-file2 {input.reverse} " # -r: Input paired-end reverse fastq file
+ "--gzip-output " # -g: Output gzipped files
+ "--output-pe1 {output.forward} " # -o: Output trimmed forward fastq file
+ "--output-pe2 {output.reverse} " # -p: Output trimmed reverse fastq file (must use -s option)
+ "--output-single {output.single} " # -s: Output trimmed singles fastq file
+ "&> {log}" # Add redirection for log
###############################################################################
rule cutadapt:
--
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