Merge pull request #391 from JoseEspinosa/updates

Get rid of lib to merge tools v2.14.1

Author: bjlang

.nf-core.yml

@@ -5,3 +5,8 @@ lint:
     - config_defaults:
         - params.bamtools_filter_se_config
         - params.bamtools_filter_pe_config
+  files_unchanged:
+    - .github/CONTRIBUTING.md
+    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml

CHANGELOG.md

@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10).
 - [[#367](https://github.com/nf-core/chipseq/issues/367)] - Get rid of `CheckIfExists` for params paths.
 - [[#370](https://github.com/nf-core/chipseq/issues/370)] - Fix stack overflow exceptions in phantompeakqualtools ([see here](https://github.com/kundajelab/phantompeakqualtools/issues/3)).
+- [[PR #391](https://github.com/nf-core/chipseq/pull/391)] - Get rid of the `lib` folder and rearrange the pipeline accordingly.
 
 ### Software dependencies
 

conf/base.config

@@ -57,7 +57,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }

conf/modules.config

@@ -30,14 +30,6 @@ process {
         ]
     }
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
     withName: 'KHMER_UNIQUEKMERS' {
         publishDir = [ enabled: false ]
     }