Change Sickle-trim option for one letter than --word because issue segmentation fault 11

README.md

@@ -13,7 +13,7 @@ RQCP check NGS (illumina) reads quality and clean it if needed, as you set, usin
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workflow/rules/reads_quality_control_pipeline.smk

@@ -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
-        "--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
+       "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-threshold: 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
 
 ###############################################################################
 rule cutadapt: