Add bwa.tar.gz extraction to RQCP.sh

RQCP.sh

@@ -14,7 +14,7 @@ echo "Latest modification: 2021.10.05"
 echo "Todo: na"
 echo "________________________________________________________________________"
 
-###### Hardware check #####
+##### Hardware check #####
 echo ""
 echo "##### HARDWARE #####"
 echo "--------------------"
@@ -27,7 +27,7 @@ ramsize=$(expr $hwmemsize / $((1024**3))) # 1024**3 = GB
 echo "System Memory: ${ramsize} GB"       # Print RAM size
 echo "________________________________________________________________________"
 
-###### Working directory
+##### Working directory #####
 echo ""
 echo "##### WORKING DIRECTORY #####"
 echo "-----------------------------"
@@ -35,26 +35,59 @@ WORKDIR=${0%/*}
 echo "CWD: ${WORKDIR}"
 echo "________________________________________________________________________"
 
-###### Rename samples, comment first line if you want do keep barcode-ID in name
+###### Rename samples #####
+# comment first line if you want do keep barcode-ID in name
+echo ""
+echo "##### RENAME FASTQ FILES #####"
+echo "------------------------------"
 rename -v 's/_S\d+_/_/' ${WORKDIR}/resources/reads/*.fastq.gz 2> /dev/null                # Remove barcode-ID like {_S001_}
 rename -v 's/_L\d+_/_/' ${WORKDIR}/resources/reads/*.fastq.gz 2> /dev/null                # Remove line-ID ID like {_L001_}
 rename -v 's/_\d+.fastq.gz/.fastq.gz/' ${WORKDIR}/resources/reads/*.fastq.gz 2> /dev/null # Remove end-name ID like {_001}.fastq.gz
+echo "Done."
+echo "________________________________________________________________________"
 
-###### Create links for rax samples
+###### Create links for raw samples #####
+echo ""
+echo "##### CREATE RAW READ LINKS #####"
+echo "---------------------------------"
 mkdir ${WORKDIR}/results/ ${WORKDIR}/results/reads/ ${WORKDIR}/results/reads/raw/ 2> /dev/null
 for FASTQ in ${WORKDIR}/resources/reads/*.fastq.gz ; do ln -s $FASTQ ${WORKDIR}/results/reads/raw/$(basename $FASTQ) 2> /dev/null ; done # Create Symbol links
+echo "Done."
+echo "________________________________________________________________________"
 
-##### Create dir for QC
+###### Create dir for QC tools #####
 mkdir ${WORKDIR}/results/reads/cutadapt/ ${WORKDIR}/results/reads/sickle-trim/ ${WORKDIR}/results/reads/fastq-join/ 2> /dev/null
 
-###### Call snakemake pipeline
+###### Extract bwa indexes for small genomes #####
+echo ""
+echo "##### BWA INDEXES EXTRATION #####"
+echo "---------------------------------"
+tar -xzvf ${WORKDIR}/resources/databases/bwa.tar.gz && rm -f ${WORKDIR}/resources/databases/bwa.tar.gz
+echo "________________________________________________________________________"
+
+###### Call snakemake pipeline #####
+echo ""
+echo "##### SNAKEMAKE PIPELIE #####"
+echo "-----------------------------"
+echo ""
+echo "Unlocking working directory:"
 snakemake --directory ${WORKDIR} --use-conda --keep-going --rerun-incomplete -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --cores --unlock # unlock first, if previous error
+echo ""
+echo "Dry run:"
 snakemake --directory ${WORKDIR} --use-conda --keep-going --rerun-incomplete -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --cores --dryrun # then dry run, check error like missing file
+echo ""
+echo "Let's go!"
 snakemake --directory ${WORKDIR} --use-conda --keep-going --rerun-incomplete -s ${WORKDIR}/workflow/rules/reads_quality_control_pipeline.smk --cores          # at last, real run 
+echo "________________________________________________________________________"
 
 ###### Create usefull graphs and summary
+echo ""
+echo "##### SNAKEMAKE PIPELINE GRAPHS ######"
+echo "--------------------------------------"
 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
+echo "Done."
+echo "________________________________________________________________________"