Move previous tests for inputs into the format of template 2.13.1

[rannick]

// Check mandatory parameters

// //TODO: move this to utils_nf_core_rnafusion_pipeline // if (file(params.input).exists() || params.build_references) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet does not exist or was not specified!' } // if (params.fusioninspector_only && !params.fusioninspector_fusions) { exit 1, 'Parameter --fusioninspector_fusions PATH_TO_FUSION_LIST expected with parameter --fusioninspector_only'} // if (params.tools_cutoff < 1) { exit 1, 'Parameter: --tools_cutoff should be >= 1'}

Description of feature

// def checkPathParamList = [ // params.fasta, // params.fai, // params.gtf, // params.transcript, // ]

// for (param in checkPathParamList) if ((param) && !params.build_references) file(param, checkIfExists: true) // def params_fasta_path_uri = params.fasta =~ /^([a-zA-Z0-9])://(?:[-a-zA-Z0-9()@:%_+.~#?&/=])$/ // // check if params.fasta is a remote uri such as s3://, gs:// or dx:// // if (params_fasta_path_uri){ // log.info "INFO: a remote uri path detected, check for absolute path and trailing '/' not performed" // // log.info "INFO: remote uri path detected (e.g. s3), check for absolute path and trailing '/' not performed" // } // else { // for (param in checkPathParamList) if ((param.toString())!= file(param).toString() && !params.build_references) { exit 1, "Problem with ${param}: ABSOLUTE PATHS are required! Check for trailing '/' at the end of paths too." } // }