Merge pull request #265 from nf-core/gsea_html_fix

GSEA- pngs and htmls in same place

CHANGELOG.md

@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [[#265](https://github.com/nf-core/differentialabundance/pull/265) - GSEA- pngs and htmls in same place ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#257](https://github.com/nf-core/differentialabundance/pull/257)] - Fixed FILTER_DIFFTABLE module, updated PROTEUS module to better handle whitespace in prefix param, made docs clearer ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#254](https://github.com/nf-core/differentialabundance/pull/254)] - Made differential_file_suffix optional ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#240](https://github.com/nf-core/differentialabundance/pull/240)] - Publish GSEA reports ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))

conf/modules.config

@@ -295,19 +295,9 @@ process {
         ext.prefix = { "${meta.id}.${gene_sets.baseName}." }
         publishDir = [
             [
-                path: { "${params.outdir}/tables/gsea/${meta.id}/${gene_sets.baseName}" },
+                path: { "${params.outdir}/report/gsea/${meta.id}/${gene_sets.baseName}" },
                 mode: params.publish_dir_mode,
-                pattern: '*gsea_report_for_*.tsv'
-            ],
-            [
-                path: { "${params.outdir}/plots/gsea/${meta.id}/${gene_sets.baseName}" },
-                mode: params.publish_dir_mode,
-                pattern: '*.png'
-            ],
-            [
-                path: { "${params.outdir}/html/gsea/${meta.id}/${gene_sets.baseName}" },
-                mode: params.publish_dir_mode,
-                pattern: '*.{html,zip}'
+                pattern: '*.{html,zip,png,tsv,rpt}'
             ]
         ]
         ext.args = { [