diff --git a/modules/local/scaffolds_samplesheet_check.nf b/modules/local/scaffolds_samplesheet_check.nf index cd701ae0..084bf95b 100644 --- a/modules/local/scaffolds_samplesheet_check.nf +++ b/modules/local/scaffolds_samplesheet_check.nf @@ -12,22 +12,19 @@ process SCAFFOLDS_SAMPLESHEET_CHECK { path "versions.yml", emit: versions script: // This script is bundled with the pipeline, in cdcgov/phoenix/bin/ - // Adding if/else for if running on ICA it is a requirement to state where the script is, however, this causes CLI users to not run the pipeline from any directory. - if (params.ica==false) { ica = "" } - else if (params.ica==true) { ica = "python ${workflow.launchDir}/bin/" } - else { error "Please set params.ica to either \"true\" if running on ICA or \"false\" for all other methods." } // define variables def container_version = "base_v2.1.0" def container = task.container.toString() - "quay.io/jvhagey/phoenix@" + def script = params.ica ? "python ${params.ica_path}/check_assembly_samplesheet.py" : "check_assembly_samplesheet.py" """ - ${ica}check_assembly_samplesheet.py \\ + ${script} \\ $samplesheet \\ samplesheet.valid.csv cat <<-END_VERSIONS > versions.yml "${task.process}": python: \$(python --version | sed 's/Python //g') - check_assembly_samplesheet.py: \$(${ica}check_assembly_samplesheet.py --version ) + check_assembly_samplesheet.py: \$(${script} --version ) phoenix_base_container_tag: ${container_version} phoenix_base_container: ${container} END_VERSIONS