diff --git a/README.md b/README.md index 2035c8f12db770ae3e2f90ba3f7cd16753abff97..1d1885181cef0024897cdf1f399b86632ce9cd64 100755 --- a/README.md +++ b/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 diff --git a/main.nf b/main.nf index 973d5ed7de916f0b67591d952f9afcac7693d1a6..cb3cd401a742bdc61e63b638c17040bce905299d 100755 --- a/main.nf +++ b/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" diff --git a/nextflow.config b/nextflow.config index 32498e3efcb7a8eea9da9a43c03ad8ff6b828189..fe17f344db676a4fa25896dd6d6aae43abcc1940 100755 --- a/nextflow.config +++ b/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" }