Merge branch 'CW-4192' into 'dev'

params to margs for polyA [CW-4192]

Closes CW-4192

See merge request epi2melabs/workflows/wf-basecalling!73

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v1.2.2]
+### Changes
+- Bug fix for downstream workflows and `--poly_a_config` which does not affect normal workflow use.
+
 ## [v1.2.1]
 ### Added
 - Output channel for demuxed BAM files for downstream use.

lib/signal/ingress.nf

@@ -289,7 +289,7 @@ workflow wf_dorado {
         // Deal with a Poly(A) configs. If config is present then turn on Poly(A) calling
         Boolean do_estimate_poly_a = false
         if (margs.poly_a_config ){
-            poly_a_config = file(params.poly_a_config, checkIfExists: true)
+            poly_a_config = file(margs.poly_a_config, checkIfExists: true)
             do_estimate_poly_a = true
         } else {
             poly_a_config = file("${projectDir}/data/OPTIONAL_FILE")

nextflow.config

@@ -87,7 +87,7 @@ manifest {
     description     = 'Helper workflow for basecalling ONT reads.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = '1.2.1'
+    version         = '1.2.2'
 }
 
 epi2melabs {