release v6.1.0: config file debugged

README.md

@@ -192,6 +192,12 @@ Gitlab developers
 
 ## WHAT'S NEW IN
 
+
+### v6.1.0
+
+1) config file debugged
+
+
 ### v6.0.0
 
 1) Ok up to q20 tested using the test file

main.nf

@@ -68,7 +68,7 @@ if(system_exec == 'local' || system_exec == 'slurm'){
     }
     def file_exists3 = ref_genome_ch_test.exists()
     if( ! file_exists3){
-        error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID ref_genome PARAMETER IN nextflow.config FILE: ${ref_genome}\n\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\nTHE REFERENCE GENOME MUST HAVE BEEN REFERENCED\n\n========\n\n"
+        error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID ref_genome PARAMETER IN nextflow.config FILE: ${ref_genome}\n\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\nTHE REFERENCE GENOME MUST HAVE BEEN REFERENCED (.bt FILES PRESENTS) AND INDEXED (.fai FILE PRESENT)\n\n========\n\n"
     }
 }else{
     error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID system_exec PARAMETER IN nextflow.config FILE: ${system_exec}\n\n========\n\n"

nextflow.config

@@ -46,7 +46,7 @@ env {
     added_nb=3 // number of nucleotids taken after fivep_seq_nb for graphic display, to see that the frequency of each base tends toward 0.25 after fivep_seq_nb on the graph
     //// end fivep_filtering
     cutoff_nb=25 // reads of length cutoff_nb after trimming are removed
-    ref_genome="/pasteur/homes/gmillot/reference_genomes/coli_K12_MG1655_NC_000913.3_ORI_CENTERED/Ecoli-K12-MG1655_ORI_CENTERED"
+    ref_genome="/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/coli_K12_MG1655_NC_000913.3_ORI_CENTERED/Ecoli-K12-MG1655_ORI_CENTERED"
     cute_path="https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v10.9.0/cute_little_R_functions.R" // single character string indicating the file (and absolute pathway) of the required cute_little_R_functions toolbox. With ethernet connection available, this can also be used: "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v5.1.0/cute_little_R_functions.R" or local "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
 }