Passing tests

Start_Quality.sh

 #!/bin/bash
 
+##### colors ######
+red="\033[1;31m"   # red
+green="\033[1;32m" # green
+ylo="\033[1;33m"   # yellow
+blue="\033[1;34m"  # blue
+nc="\033[0m"       # no color
+
 ###### About ######
 echo ""
 echo "##### ABOUT #####"
@@ -10,7 +17,7 @@ echo "Author: Nicolas Fernandez"
 echo "Affiliation: IRD_U233_TransVIHMI"
 echo "Aim: Bash script for RQC pipeline"
 echo "Date: 2021.04.30"
-echo "Run: snakemake --snakemake rqc.smk --cores --use-conda"
+echo "Run: snakemake --snakemake reads_quality_control.smk --cores --use-conda"
 echo "Latest modification: 2022.01.27"
 echo "Todo: done"
 echo "________________________________________________________________________"
@@ -76,13 +83,23 @@ echo "##### SNAKEMAKE PIPELINE #####"
 echo "-----------------------------"
 echo ""
 
+echo "Unlocking working directory:"
+# Specify working directory (relative paths in the snakefile will use this as their origin).
+# The workflow definition in form of a snakefile.
+# Remove a lock on the working directory.
+snakemake \
+    --directory ${workdir} \
+    --snakefile ${workdir}/workflow/rules/reads_quality_control.smk \
+    --unlock
+
+echo ""
 echo "Conda environments list:"
 # Specify working directory (relative paths in the snakefile will use this as their origin).
 # The workflow definition in form of a snakefile.
 # List all conda environments and their location on disk.
 snakemake \
     --directory ${workdir}/ \
-    --snakefile ${workdir}/workflow/rules/rqc.smk \
+    --snakefile ${workdir}/workflow/rules/reads_quality_control.smk \
     --list-conda-envs
 
 echo ""
@@ -93,7 +110,7 @@ echo "Conda environments update:"
 # Cleanup unused conda environments.
 snakemake \
     --directory ${workdir}/ \
-    --snakefile ${workdir}/workflow/rules/rqc.smk \
+    --snakefile ${workdir}/workflow/rules/reads_quality_control.smk \
     --cores \
     --conda-cleanup-envs
 
@@ -107,23 +124,12 @@ echo "Conda environments setup:"
 # If mamba package manager is not available, or if you still prefer to use conda, you can enforce that with this setting (default: 'mamba').
 snakemake \
     --directory ${workdir}/ \
-    --snakefile ${workdir}/workflow/rules/rqc.smk \
+    --snakefile ${workdir}/workflow/rules/reads_quality_control.smk \
     --cores \
     --use-conda \
     --conda-create-envs-only \
     --conda-frontend mamba
 
-
-echo ""
-echo "Unlocking working directory:"
-# Specify working directory (relative paths in the snakefile will use this as their origin).
-# The workflow definition in form of a snakefile.
-# Remove a lock on the working directory.
-snakemake \
-    --directory ${workdir} \
-    --snakefile ${workdir}/workflow/rules/rqc.smk \
-    --unlock
-
 echo ""
 echo "Dry run:"
 # Specify working directory (relative paths in the snakefile will use this as their origin).
@@ -134,7 +140,7 @@ echo "Dry run:"
 # Do not execute anything, and display what would be done. If you have a very large workflow, use –dry-run –quiet to just print a summary of the DAG of jobs. 
 snakemake \
     --directory ${workdir} \
-    --snakefile ${workdir}/workflow/rules/rqc.smk \
+    --snakefile ${workdir}/workflow/rules/reads_quality_control.smk \
     --cores 1 \
     --use-conda \
     --dryrun \
@@ -153,7 +159,7 @@ echo "Let's go!"
 # Tell the scheduler to assign creation of given targets (and all their dependencies) highest priority.
 snakemake \
     --directory ${workdir} \
-    --snakefile ${workdir}/workflow/rules/rqc.smk \
+    --snakefile ${workdir}/workflow/rules/reads_quality_control.smk \
     --cores \
     --use-conda \
     --printshellcmds \
@@ -168,7 +174,7 @@ echo "##### SNAKEMAKE PIPELINE GRAPHS ######"
 echo "--------------------------------------"
 echo ""
 
-mkdir ${workdir}/results/summary/ 2> /dev/null
+mkdir ${workdir}/results/reports/graphs/ 2> /dev/null
 
 graphList="dag rulegraph filegraph"
 extentionList="pdf png"
@@ -177,17 +183,17 @@ for graph in ${graphList} ; do
     for extention in ${extentionList} ; do
         snakemake \
             --directory ${workdir}/ \
-            --snakefile ${workdir}/workflow/rules/rqc.smk \
+            --snakefile ${workdir}/workflow/rules/reads_quality_control.smk \
             --${graph} | \
             dot -T${extention} > \
-                ${workdir}/results/summary/${graph}.${extention} ;
+                ${workdir}/results/reports/graphs/${graph}.${extention} ;
     done ;
 done
 
 snakemake \
     --directory ${workdir} \
-    --snakefile ${workdir}/workflow/rules/rqc.smk \
-    --summary > ${workdir}/results/summary/files_summary.txt
+    --snakefile ${workdir}/workflow/rules/reads_quality_control.smk \
+    --summary > ${workdir}/results/reports/files_summary.txt
 
 echo "________________________________________________________________________"
 

workflow/rules/rqc.smk → workflow/rules/reads_quality_control.smk

 ###############################################################################
-# Name: RQC pipeline
+# Name: reads_quality_control.smk
 # Author: Nicolas Fernandez
 # Affiliation: IRD_U233_TransVIHMI
-# Aim: Snakefile for RQC pipeline
+# Aim: Snakefile for Reads Quality Control pipeline
 # Date: 2021.04.30
-# Run: snakemake --snakefile rqc.smk --cores --use-conda 
+# Run: snakemake --snakefile reads_quality_control.smk --cores --use-conda 
 # Latest modification: 2022.01.25
 # Todo: done