ISSUE: solved the local variable by removing the unused function

Dockerfile

@@ -1,4 +1,4 @@
-FROM continuumio/miniconda3:23.5.2-0 AS build
+FROM continuumio/miniconda3:25.3.1-1 as build
 
 LABEL authors="andrea.talenti@ed.ac.uk" \
       description="Docker image containing base requirements for nf-LO pipelines"
@@ -35,7 +35,9 @@ RUN /venv/bin/conda-unpack
 # The runtime-stage image; we can use Debian as the
 # base image since the Conda env also includes Python
 # for us.
-FROM debian:buster AS runtime
+FROM debian:bookworm AS runtime
+
+RUN echo "deb http://archive.debian.org/debian/ stretch contrib main non-free" | tee -a /etc/apt/sources.list
 
 # Install procps in debian to make it compatible with reporting
 RUN apt-get update && \

modules/processes/postprocess/main.nf

@@ -155,38 +155,6 @@ process chainMerge {
     """
 }
 
-process chainNet_old{
-    tag "chainnet"
-    publishDir "${params.outdir}/chainnet", mode: 'copy', overwrite: true
-    label 'medium'
-
-    input:
-        path rawchain  
-        path twoBitS
-        path twoBitT
-        path twoBitsizeS
-        path twoBitsizeT
-
-    output: 
-        path "liftover.chain", emit: liftover_ch  
-        path "netfile.net", emit: netfile_ch  
-
-    script:
-    if ( params.aligner != "blat" & params.aligner != "nucmer" & params.aligner != "GSAlign")
-    def haplotypes = params.haplotypes ? "-inclHap" : ""
-    """
-    chainPreNet ${haplotypes} {rawchain} ${twoBitsizeS} ${twoBitsizeT} stdout |
-        chainNet -verbose=0 ${haplotypes} stdin ${twoBitsizeS} ${twoBitsizeT} stdout /dev/null | netSyntenic stdin netfile.net
-    netChainSubset -verbose=0 netfile.net ${rawchain} stdout | chainStitchId stdin stdout > liftover.chain
-    """
-
-    stub:
-    """
-    touch liftover.chain
-    touch netfile.net
-    """
-}
-
 process chainNet{
     tag "chainnet"
     publishDir "${params.outdir}/chainnet", mode: 'copy', overwrite: true
@@ -552,4 +520,4 @@ process make_report {
     """
     touch chainMetrics.html
     """
-}
+}