Same as Sickle, replace fastq-screen --quiet option with shortcut -q to avoid segmentatin fault 11

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

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: