Fixed 'q' insertion L.127 disabling right conda environment creation

Start_GeVarLi.sh

@@ -124,7 +124,7 @@ Conda environment ${red}snakemake-base_v.${snakemake_base_version}${nc} will be
     # ${red}Rename${nc}:    Rename fastq files (ver. 1.601)
     # ${red}Graphviz${nc}:  Dot snakemake DAG (ver. 7.1.0)
 "
-q    conda env create -f ${workdir}/workflow/environments/${os}/snakemake-base_v.${snakemake_base_version}.yaml
+    conda env create -f ${workdir}/workflow/environments/${os}/snakemake-base_v.${snakemake_base_version}.yaml
 fi
 
 # Remove old 'gevarli' and 'snakemake' environments

configuration/config.yaml

@@ -25,9 +25,9 @@ consensus:
   min_cov: # Minimum coverage, mask lower regions with "N" (default: "30") [INT]
   # Available options (not exhaustive), choose one:
     - '30'                         # AFROSCREEN SARS-CoV-2 Illumina amplicons sequencing (default)
-    #- 'Add_your_minimum_coverage' # Custom
+    #- 'Add_your_minimum_coverage' # Custom 
   min_af: '0.2'               # Minimum allele frequency allowed (default: "0.2") [FLOAT]
-  reference:                 # Your reference, in fasta format (default: SARS-CoV-2_Wuhan_MN-908947-3)
+  reference: # Your reference, in fasta format (default: SARS-CoV-2_Wuhan_MN-908947-3)
   # Available options (not exhaustive), choose one:
     - 'SARS-CoV-2_Wuhan_MN-908947-3'       # SARS-CoV-2 (Nextclade and Pangolin)
     #- 'Monkeypox-virus_Zaire_AF-380138-1'  # Monkeypox  (Nextclade and Pangolin)

workflow/snakefiles/gevarli.smk

@@ -36,6 +36,8 @@ def get_nextclade_input(wildcards):
 ###############################################################################
 ###### WILDCARDS ######
 
+#SAMPLE, = glob_wildcards("/users/illumina/local/data/run_1/FATSQ/{sample}_R1.fastq.gz")
+
 SAMPLE, = glob_wildcards("resources/reads/{sample}_R1.fastq.gz")
 
 ###############################################################################
@@ -861,6 +863,8 @@ rule cutadapt_adapters_removing:
     input:
         fwd_reads = "resources/reads/{sample}_R1.fastq.gz",
         rev_reads = "resources/reads/{sample}_R2.fastq.gz"
+        #fwd_reads = "/users/illumina/local/data/run_1/FATSQ/{sample}_R1.fastq.gz",
+        #rev_reads = "/users/illumina/local/data/run_1/FATSQ/{sample}_R2.fastq.gz"
     output:
         fwd_reads = temp("results/01_Trimming/cutadapt/{sample}_cutadapt-removed_R1.fastq.gz"),
         rev_reads = temp("results/01_Trimming/cutadapt/{sample}_cutadapt-removed_R2.fastq.gz")