Merge pull request nf-cmgg#32 from ToonRosseel/dev

bump version 1.2.1
ToonRosseel · Jan 7, 2025 · ea2f61a · ea2f61a
2 parents d748611 + 08b5b33
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.2.1dev
+## v1.2.1 Lunatic Lamkel Zé [2025-01-07]
 
 ### `Improvements`
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-cmgg/exomecnv/tree/dev" target="_blank">nf-cmgg/exomecnv</a>
+  This report has been generated by the <a href="https://github.com/nf-cmgg/exomecnv/releases/tag/1.2.1" target="_blank">nf-cmgg/exomecnv</a>
   analysis pipeline.
 report_section_order:
   "nf-cmgg-exomecnv-methods-description":

diff --git a/docs/output.md b/docs/output.md
@@ -24,15 +24,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 ### Cram Prepare
 
-If CRAM/CRAI files were provided in the samplesheet, they will be converted into BAM/BAI first before continuing with the pipeline. If the directive `publishDir` option `enabled` is set to `true` (default: `false`) , the BAM/BAI are in the output folder (subfolder `bam/`).
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `bam/`
-  - `<sample>.bam`: BAM file
-  - `<sample>.bam.bai`: BAI index file
-  </details>
+If CRAM/CRAI files were provided in the samplesheet, they will be converted into BAM/BAI first before continuing with the pipeline.
 
 ### ExomeDepth count
 

diff --git a/nextflow.config b/nextflow.config
@@ -247,7 +247,7 @@ manifest {
     description     = """A nextflow pipeline for calling exome CNVs"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.10.0'
-    version         = '1.2.1dev'
+    version         = '1.2.1'
     doi             = ''
 }
 

diff --git a/tests/pipeline/annotate/main.nf.test.snap b/tests/pipeline/annotate/main.nf.test.snap
@@ -30,7 +30,7 @@
                     "tabix": 1.2
                 },
                 "Workflow": {
-                    "nf-cmgg/exomecnv": "v1.2.1dev"
+                    "nf-cmgg/exomecnv": "v1.2.1"
                 }
             },
             [
@@ -198,7 +198,7 @@
                 "samplesheet.csv:md5,c759d9162a7bf9ad1d3eba088ecd46bf"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -207,4 +207,4 @@
         },
         "timestamp": "2024-11-27T08:44:26.575986"
     }
-}
+}
diff --git a/tests/pipeline/callers/main.nf.test.snap b/tests/pipeline/callers/main.nf.test.snap
@@ -31,7 +31,7 @@
                     "tabix": 1.2
                 },
                 "Workflow": {
-                    "nf-cmgg/exomecnv": "v1.2.1dev"
+                    "nf-cmgg/exomecnv": "v1.2.1"
                 }
             },
             [
@@ -157,7 +157,7 @@
                     "tabix": 1.2
                 },
                 "Workflow": {
-                    "nf-cmgg/exomecnv": "v1.2.1dev"
+                    "nf-cmgg/exomecnv": "v1.2.1"
                 }
             },
             [
@@ -254,4 +254,4 @@
         },
         "timestamp": "2024-11-27T08:55:14.228024"
     }
-}
+}
diff --git a/tests/pipeline/default/main.nf.test.snap b/tests/pipeline/default/main.nf.test.snap
@@ -4,7 +4,7 @@
             1,
             {
                 "Workflow": {
-                    "nf-cmgg/exomecnv": "v1.2.1dev"
+                    "nf-cmgg/exomecnv": "v1.2.1"
                 }
             },
             [
@@ -30,4 +30,4 @@
         },
         "timestamp": "2024-11-27T08:41:45.372688"
     }
-}
+}