Release v.2023.06

Start_GeVarLi.sh

@@ -535,9 +535,9 @@ ${green}#####${nc} ${red}CLEAN & SAVE${nc} ${green}#####${nc}
 ${green}------------------------${nc}
 "
 
-# Save and Deactive Snakemake-Base environment
-cp ${workdir}/workflow/environments/${os}/gevarli-tools_v.*.yaml ${workdir}/results/10_Reports/
-cp ${workdir}/workflow/environments/${os}/snakemake-base_v.*.yaml ${workdir}/results/10_Reports/
+# Save and deactive environments
+mkdir -p ${workdir}/results/10_Reports/conda_env/ 2> /dev/null
+cp ${workdir}/workflow/environments/${os}/*.yaml ${workdir}/results/10_Reports/conda_env/
 conda deactivate
 
 # Cleanup

configuration/config.yaml

@@ -102,11 +102,11 @@ fastq_screen:
   subset: '10000' # Don't use whole sequences, but a subset reads (default: "10000") [INT] (0=all)
 
 ###############################################################################
-### MULTIQC ###
+### MULTIQC ### (soon)
 ###############
-multiqc:
-  config: 'configuration/multiqc/default.yaml' # Path to the multiqc configuration file
-  tag: '' # Use only modules which tagged with this keyword
+#multiqc:
+#  config: 'configuration/multiqc/default.yaml' # Path to the multiqc configuration file
+#  tag: '' # Use only modules which tagged with this keyword
 
 ###############################################################################
 ### CUTADAPT ###
@@ -160,15 +160,15 @@ bowtie2:
     #- '--large-index' # Force generated index to be "large", even if reference has fewer than 4 billion nucleotides
 
 ###############################################################################
-### GISAID ###
+### GISAID ### (soon)
 ##############
-gisaid:
-  username: 'username'
-  threshold: '30'
-  name: 'hCoV-19'
-  country: 'France'
-  identifier: ''
-  year: '2022'
+#gisaid:
+#  username: 'username'
+#  threshold: '30'
+#  name: 'hCoV-19'
+#  country: 'France'
+#  identifier: ''
+#  year: '2022'
 
 ###############################################################################
 ### ENVIRONNEMENTS ###

workflow/snakefiles/gevarli.smk

@@ -8,6 +8,7 @@
 ###                                                                         ###
 ###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
 # Name ___________________ gevarli.smk
+# Version ________________ v.2023.06
 # Author _________________ Nicolas Fernandez
 # Affiliation ____________ IRD_U233_TransVIHMI
 # Aim ____________________ Snakefile with GeVarLi rules

workflow/snakefiles/indexing_genomes.smk

@@ -8,6 +8,7 @@
 ###                                                                         ###
 ###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
 # Name ___________________ indexing_genomes.smk
+# Version ________________ v.2023.06
 # Author _________________ Nicolas Fernandez
 # Affiliation ____________ IRD_U233_TransVIHMI
 # Aim ____________________ Snakefile with indexing genomes rules

workflow/snakefiles/quality_control.smk

@@ -8,6 +8,7 @@
 ###                                                                         ###
 ###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
 # Name ___________________ quality_control.smk
+# Version ________________ v.2023.06
 # Author _________________ Nicolas Fernandez
 # Affiliation ____________ IRD_U233_TransVIHMI
 # Aim ____________________ Snakefile with quality control rules