Just text edit RQCP.sh print

.gitignore

@@ -2,7 +2,7 @@
 ~*
 *#
 .DS_Store
-#.snakemake
+.snakemake
 *.temp
 *.fastq
 *.fastq.gz

RQCP.sh

@@ -87,7 +87,7 @@ mkdir ${workdir}/results/reads/raw_links/ 2> /dev/null
 # Create Symbolic links for raw reads
 
 for fastq in ${workdir}/resources/reads/*.fastq.gz ; do
-    ln --force --symbolic $fastq ${workdir}/results/reads/raw_links/$(basename $fastq) ;
+    ln -sFv $fastq ${workdir}/results/reads/raw_links/$(basename $fastq) ;
 done
 
 echo "________________________________________________________________________"
@@ -102,24 +102,24 @@ rename --force --verbose 's/_S\d+_L00\d_/_/' ${workdir}/results/reads/raw_links/
 rename --force --verbose 's/_001.fastq.gz/.fastq.gz/' ${workdir}/results/reads/raw_links/*.fastq.gz  # Remove end-name ID like {_001}.fastq.gz
 
 # Create dir for QC-tools and Conf-backup #####
-mkdir ${workdir}/results/reads/cutadapt_removed/
-mkdir ${workdir}/results/reads/sickle-trim_paired-end_filtered/
-mkdir ${workdir}/results/reads/fastq-join_single-end/
-mkdir ${workdir}/results/reads/all_merged_single-end/
-cp -R ${workdir}/config/ ${workdir}/results/config/
+mkdir ${workdir}/results/reads/cutadapt_removed/ 2> /dev/null
+mkdir ${workdir}/results/reads/sickle-trim_paired-end_filtered/ 2> /dev/null
+mkdir ${workdir}/results/reads/fastq-join_single-end/ 2> /dev/null
+mkdir ${workdir}/results/reads/all_merged_single-end/ 2> /dev/null
+cp -R ${workdir}/config/ ${workdir}/results/config/ 2> /dev/null
 
 echo "________________________________________________________________________"
 
 
 ###### Extract bwa indexes for small genomes #####
 echo ""
-echo "##### BOWTIE2 INDEXES EXTRACTION #####"
+echo "##### INDEXES EXTRACTION #####"
 echo "---------------------------------"
 
 #tar --keep-old-files -xzvf ${workdir}/resources/databases/bowtie2_small_genomes.tar.gz -C ${workdir}/resources/databases/
 #tar --keep-old-files -xzvf ${workdir}/resources/databases/bowtie2_large_genomes.tar.gz -C ${workdir}/resources/databases/
 tar --keep-old-files -xzvf ${workdir}/resources/databases/bwa_small_genomes.tar.gz -C ${workdir}/resources/databases/
-tar --keep-old-files -xzvf ${workdir}/resources/databases/bwa_large_genomes.tar.gz -C ${workdir}/resources/databases/
+#tar --keep-old-files -xzvf ${workdir}/resources/databases/bwa_large_genomes.tar.gz -C ${workdir}/resources/databases/
 
 echo "________________________________________________________________________"