diff --git a/main.nf b/main.nf index c3f6c02..210d26c 100644 --- a/main.nf +++ b/main.nf @@ -192,7 +192,6 @@ workflow { 'narrow', params.encyclopedia.chromatogram.params ) - encyclopedia_version = encyclopeda_export_elib.out.encyclopedia_version quant_library = encyclopeda_export_elib.out.elib @@ -216,8 +215,9 @@ workflow { ) - final_elib = encyclopedia_quant.out.elib + encyclopedia_version = encyclopedia_quant.out.encyclopedia_version + final_elib = encyclopedia_quant.out.elib all_elib_ch = all_elib_ch.concat( encyclopedia_quant.out.individual_elibs, encyclopedia_quant.out.elib, @@ -412,7 +412,7 @@ def is_panorama_used() { (params.quant_spectra_dir && any_entry_is_panorama(params.quant_spectra_dir)) || (params.chromatogram_library_spectra_dir && any_entry_is_panorama(params.chromatogram_library_spectra_dir)) || (params.skyline_skyr_file && any_entry_is_panorama(params.skyline_skyr_file)) - + } // diff --git a/workflows/save_run_details.nf b/workflows/save_run_details.nf index eca2043..e272680 100644 --- a/workflows/save_run_details.nf +++ b/workflows/save_run_details.nf @@ -38,15 +38,17 @@ workflow save_run_details { main: - // split program version variable names and value + // Read version txt files and create a channel of variable name, value pairs version_vars = version_files.map{ program -> program.collect{ it -> - elems = it.split('=') - [elems[0].strip(), elems[1].strip()] + elems = it.split('=').collect{ str -> + str.strip().replaceAll(/^['"]|['"]$/, '') + } + [elems[0], elems[1]] } } - + // Create channel of workflow run metadata workflow_vars = Channel.fromList([["Nextflow run at", workflow.start], ["Nextflow version", nextflow.version], ["Workflow git address", "${workflow.repository}"], @@ -55,9 +57,13 @@ workflow save_run_details { ["Run session ID", workflow.sessionId], ["Command line", workflow.commandLine]]) + // Create channel of docker image names and paths + docker_images = Channel.fromList(params.images.collect{k, v -> ["${k} docker image", v]}) + all_vars = workflow_vars.concat( input_files.flatten().collate(2), - version_vars.flatten().collate(2) + version_vars.flatten().collate(2), + docker_images ) var_names = all_vars.map{ it -> it[0] }