Update MultiQC to 1.13 (from 1.12)

README.md

@@ -474,7 +474,7 @@ Intellectual property belongs to [IRD](https://www.ird.fr/) and authors.
       │    │    ├── 🍜 pangolin_v.4.0.6.yaml
       │    │    ├── 🍜 samtools_v.1.15.1.yaml
       │    │    └── 🍜 sickle-trim_v.1.33.yaml
-      └── 📂 rules/
+      └── 📂 snakefiles/
 	       ├── 📜 gevarli.smk
 	       ├── 📜 indexing_genomes.smk
            └── 📜 quality_control.smk

Start_GeVarLi.sh

@@ -263,7 +263,7 @@ for snakefile in ${snakefile_list} ; do
     echo -e "${blue}-- ${snakefile} --${nc}" ;
     snakemake \
 	--directory ${workdir}/ \
-        --snakefile ${workdir}/workflow/rules/${snakefile}.smk \
+        --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
         --config os=${os} \
         --rerun-incomplete \
         --unlock ;
@@ -284,7 +284,7 @@ for snakefile in ${snakefile_list} ; do
     echo -e "${blue}-- ${snakefile} --${nc}" ;
     snakemake \
         --directory ${workdir}/ \
-        --snakefile ${workdir}/workflow/rules/${snakefile}.smk \
+        --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
         --cores ${max_threads} \
         --config os=${os} \
         --rerun-incomplete \
@@ -309,7 +309,7 @@ for snakefile in ${snakefile_list} ; do
     echo -e "${blue}-- ${snakefile} --${nc}" ;
     snakemake \
         --directory ${workdir}/ \
-        --snakefile ${workdir}/workflow/rules/${snakefile}.smk \
+        --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
         --cores ${max_threads} \
         --config os=${os} \
         --rerun-incomplete \
@@ -338,7 +338,7 @@ for snakefile in ${snakefile_list} ; do
     echo -e "${blue}-- ${snakefile} --${nc}" ;
     snakemake \
         --directory ${workdir}/ \
-        --snakefile ${workdir}/workflow/rules/${snakefile}.smk \
+        --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
         --cores ${max_threads}\
         --config os=${os} \
         --rerun-incomplete \
@@ -355,7 +355,7 @@ ${blue}----------------${nc}
 # Specify working directory (relative paths in the snakefile will use this as their origin).
 # The workflow definition in form of a snakefile.
 # Use at most N CPU cores/jobs in parallel. If N is omitted or ‘all’, the limit is set to the number of available CPU cores.
-# Define a global maximum number of threads available to any rule. Rules requesting more threads will have their values reduced to the maximum. 
+# Define a global maximum number of threads available to any rule. Snakefiles requesting more threads will have their values reduced to the maximum. 
 # Set or overwrite values in the workflow config object.
 # Re-run all jobs the output of which is recognized as incomplete.
 # Go on with independent jobs if a job fails.
@@ -369,7 +369,7 @@ for snakefile in ${snakefile_list} ; do
     echo -e "${blue}-- ${snakefile} --${nc}" ;
     snakemake \
         --directory ${workdir}/ \
-        --snakefile ${workdir}/workflow/rules/${snakefile}.smk \
+        --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
         --cores ${max_threads} \
         --max-threads ${max_threads} \
         --config os=${os} \
@@ -474,7 +474,7 @@ for snakefile in ${snakefile_list} ; do
 	for extention in ${extention_list} ; do
 	    snakemake \
 		--directory ${workdir}/ \
-                --snakefile ${workdir}/workflow/rules/${snakefile}.smk \
+                --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
                 --${graph} \
 	    | dot -T${extention} \
             2> /dev/null \
@@ -486,7 +486,7 @@ done
 for snakefile in ${snakefile_list} ; do
     snakemake \
         --directory ${workdir} \
-        --snakefile ${workdir}/workflow/rules/${snakefile}.smk \
+        --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
         --summary > ${workdir}/results/10_Reports/files-summaries/${snakefile}_files-summary.txt \
     2> /dev/null ;
 done

config/config.yaml

@@ -44,7 +44,7 @@ conda:
     gawk:         '../envs/osx/gawk_v.5.1.0.yaml'            # Awk          ver. 5.1.0
     gevarli-base: '../envs/osx/gavarli-base_v.2022.11'       # GeVarLi-Base ver. 2022.11
     lofreq:       '../envs/osx/lofreq_v.2.1.5.yaml'          # Lofreq       ver. 2.1.5
-    multiqc:      '../envs/osx/multiqc_v.1.12.yaml'          # MultiQC      ver. 1.12
+    multiqc:      '../envs/osx/multiqc_v.1.13.yaml'          # MultiQC      ver. 1.13
     nextclade:    '../envs/osx/nextclade_v.2.8.0.yaml'       # Nextclade    ver. 2.5.0
     pangolin:     '../envs/osx/pangolin_v.4.1.3.yaml'        # Pangolin     ver. 4.1.3
     samtools:     '../envs/osx/samtools_v.1.15.1.yaml'       # Samtools     ver. 1.15.1
@@ -61,7 +61,7 @@ conda:
     gawk:         '../envs/linux/gawk_v.5.1.0.yaml'          # Awk          ver. 5.1.0
     gevarli-base: '../envs/linux/gavarli-base_v.2022.11'     # GeVarLi-Base ver. 2022.11
     lofreq:       '../envs/linux/lofreq_v.2.1.5.yaml'        # Lofreq       ver. 2.1.5
-    multiqc:      '../envs/linux/multiqc_v.1.12.yaml'        # MultiQC      ver. 1.12
+    multiqc:      '../envs/linux/multiqc_v.1.13.yaml'        # MultiQC      ver. 1.13
     nextclade:    '../envs/linux/nextclade_v.2.8.0.yaml'     # Nextclade    ver. 2.5.0
     pangolin:     '../envs/linux/pangolin_v.4.1.3.yaml'      # Pangolin     ver. 4.1.3
     samtools:     '../envs/linux/samtools_v.1.15.1.yaml'     # Samtools     ver. 1.15.1