Merge pull request #487 from drpatelh/dsl2

Fix #281

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 * Updated pipeline template to nf-core/tools `1.11`
 * Added multi-core TrimGalore support [#344](https://github.com/nf-core/rnaseq/issues/344)
+* Add nag to cite the pipeline in summary [#281](https://github.com/nf-core/rnaseq/issues/281)
 * Fixes an issue where MultiQC fails to run with `--skip_biotype_qc` option [#353](https://github.com/nf-core/rnaseq/issues/353)
 * Fixes missing Qualimap parameter `-p` [#351](https://github.com/nf-core/rnaseq/issues/351)
 * Fixes broken links [#357](https://github.com/nf-core/rnaseq/issues/357)

CITATIONS.md

@@ -1,4 +1,4 @@
-# nf-core/chipseq: Citations
+# nf-core/rnaseq: Citations
 
 ## [nf-core](https://www.ncbi.nlm.nih.gov/pubmed/32055031/)
 

lib/Checks.groovy

@@ -33,6 +33,18 @@ class Checks {
         }
     }
 
+    // Citation string
+    private static String citation(workflow) {
+        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+               "* The pipeline\n" + 
+               "  https://doi.org/10.5281/zenodo.1400710\n\n" +
+               "* The nf-core framework\n" +
+               "  https://dx.doi.org/10.1038/s41587-020-0439-x\n" +
+               "  https://rdcu.be/b1GjZ\n\n" +
+               "* Software dependencies\n" +
+               "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    }
+
     // Print a warning after SRA download has completed
     static void sra_download(log) {
         log.warn "=============================================================================\n" +

lib/Schema.groovy

@@ -84,7 +84,7 @@ class Schema {
      * Beautify parameters for --help
      */
     private static String params_help(workflow, params, json_schema, command) {
-        String output  = Headers.nf_core(workflow, params.monochrome_logs)
+        String output  = Headers.nf_core(workflow, params.monochrome_logs) + "\n"
         output        += "Typical pipeline command:\n\n"
         output        += "    ${command}\n\n"
         def params_map = params_load(json_schema)
@@ -99,8 +99,9 @@ class Schema {
             }
             output += "\n"
         }
-        output  = output.strip()
-        output += "\n" + Headers.dashed_line(params.monochrome_logs)
+        output += Headers.dashed_line(params.monochrome_logs)
+        output += "\n\n" + Checks.citation(workflow)
+        output += "\n\n" + Headers.dashed_line(params.monochrome_logs)
         return output
     }
 
@@ -173,14 +174,14 @@ class Schema {
             }
             params_summary.put(group, sub_params)
         }
-        return [ 'Core Nextflow workflow options' : workflow_summary ] << params_summary
+        return [ 'Core Nextflow options' : workflow_summary ] << params_summary
     }
 
     /*
      * Beautify parameters for summary and return as string
      */
     private static String params_summary_log(workflow, params, json_schema) {
-        String output  = Headers.nf_core(workflow, params.monochrome_logs)
+        String output  = Headers.nf_core(workflow, params.monochrome_logs) + "\n"
         def params_map = params_summary_map(workflow, params, json_schema)
         def max_chars  = params_max_chars(params_map)
         for (group in params_map.keySet()) {
@@ -193,8 +194,9 @@ class Schema {
                 output += "\n"
             }
         }
-        output  = output.strip()
-        output += "\n" + Headers.dashed_line(params.monochrome_logs)
+        output += Headers.dashed_line(params.monochrome_logs)
+        output += "\n\n" + Checks.citation(workflow)
+        output += "\n\n" + Headers.dashed_line(params.monochrome_logs)
         return output
     }