Merge pull request #295 from JoseEspinosa/updates

Fix modules.config

Author: bjlang

CHANGELOG.md

@@ -31,15 +31,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter          | New parameter      |
-| ---------------------- | ------------------ |
-| `--clusterOptions`     |                    |
-| `--conda`              | `--enable_conda`   |
-|                        | `--skip_qc`        |
-|                        | `--aligner`        |
-|                        | `--save_unaligned` |
-| `--skip_diff_analysis` | `--skip_deseq2_qc` |
-|                        | `--read_length`    |
+| Old parameter          | New parameter           |
+| ---------------------- | ----------------------- |
+| `--conda`              | `--enable_conda`        |
+| `--skip_diff_analysis` | `--skip_deseq2_qc`      |
+|                        | `--skip_qc`             |
+|                        | `--aligner`             |
+|                        | `--save_unaligned`      |
+|                        | `--read_length`         |
+|                        | `--multiqc_title`       |
+|                        | `--gff`                 |
+|                        | `--bowtie2_index`       |
+|                        | `--chromap_index`       |
+|                        | `--star_index`          |
+|                        | `--validate_params`     |
+|                        | `--show_hidden_params`  |
+|                        | `--config_profile_name` |
+| `--clusterOptions`     |                         |
+| `--single_end`         |                         |
+| `--name`               |                         |
+| `--hostnames`          |                         |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.

conf/modules.config

@@ -581,20 +581,6 @@ if (!params.skip_peak_annotation) {
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
-
-        withName: 'ANNOTATE_BOOLEAN_PEAKS' {
-            ext.prefix = { "${meta.id}_peaks" }
-            publishDir = [
-                path: { [
-                    "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                    params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                    '/consensus'
-                ].join('') },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-
-        }
     }
 
     if (!params.skip_peak_qc) {
@@ -673,6 +659,18 @@ if (!params.skip_consensus_peaks) {
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
             }
+            withName: 'ANNOTATE_BOOLEAN_PEAKS' {
+                ext.prefix = { "${meta.id}_peaks" }
+                publishDir = [
+                    path: { [
+                        "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
+                        params.narrow_peak? '/narrowPeak' : '/broadPeak',
+                        '/consensus'
+                    ].join('') },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
         }
     }