From f2ef406c1004af1c4a2962f46afa56ac5edc2141 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas=20FERNANDEZ=20NU=C3=91EZ?=
<fernandez.nunez.nicolas@gmail.com>
Date: Mon, 25 Oct 2021 15:09:49 +0200
Subject: [PATCH] Just text edit RQCP.sh print
---
.gitignore | 2 +-
RQCP.sh | 16 ++++++++--------
2 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/.gitignore b/.gitignore
index e604c3f..58b00f8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,7 +2,7 @@
~*
*#
.DS_Store
-#.snakemake
+.snakemake
*.temp
*.fastq
*.fastq.gz
diff --git a/RQCP.sh b/RQCP.sh
index fb6e0ee..8171ee6 100755
--- a/RQCP.sh
+++ b/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 "________________________________________________________________________"
--
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