Merge pull request nf-cmgg#30 from nf-cmgg/fix/bedgovcf

Fix/bedgovcf

CHANGELOG.md

@@ -3,6 +3,13 @@
 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
+
+### `Bug Fixes`
+
+- Fixed an issue where the bedgovcf yaml wasn't being given
+- Added system env fetching for `--hook_url`
+
 ## v1.2.0 - Dominant De Ketelaere [2024-11-27]
 
 ### `Updates`

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/releases/tag/1.2.0" target="_blank">nf-cmgg/exomecnv</a>
+  This report has been generated by the <a href="https://github.com/nf-cmgg/exomecnv/tree/dev" target="_blank">nf-cmgg/exomecnv</a>
   analysis pipeline.
 report_section_order:
   "nf-cmgg-exomecnv-methods-description":

main.nf

@@ -66,7 +66,7 @@ workflow {
         params.roi_auto,
         params.roi_chrx,
         params.vep_cache,
-        params.yamlconfig,
+        "${projectDir}/assets/exomedepth.yaml",
         params.multiqc_config,
         params.multiqc_logo,
         params.multiqc_methods_description,

nextflow.config

@@ -35,7 +35,7 @@ params {
     email_on_fail                = null
     plaintext_email              = false
     monochrome_logs              = false
-    hook_url                     = null
+    hook_url                     = System.getenv('HOOK_URL')
     help                         = false
     help_full                    = false
     show_hidden                  = false
@@ -58,7 +58,6 @@ params {
     roi_auto = null
     roi_chrx = null
     exomedepth = false
-    yamlconfig = null
 
     // VEP Parameters
     vep_cache_version = 105
@@ -248,7 +247,7 @@ manifest {
     description     = """A nextflow pipeline for calling exome CNVs"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.10.0'
-    version         = '1.2.0'
+    version         = '1.2.1dev'
     doi             = ''
 }
 

workflows/exomecnv.nf

@@ -133,7 +133,7 @@ workflow EXOMECNV {
 
         def bedgovcf_input = CUSTOM_MERGECNV.out.merge
             .map{ meta, bed ->
-                [meta, bed, bedgovcf_yaml]
+                [meta, bed, file(bedgovcf_yaml, checkIfExists:true)]
             }
 
         BEDGOVCF(