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

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: