luslab-umitools | Cleaned up docker files and removed groovy dependancy

tools/umi_tools/Dockerfile

@@ -1,13 +1,14 @@
 FROM continuumio/miniconda3:4.8.2
 LABEL authors="chris.cheshire@crick.ac.uk" \
       description="Docker image containing all requirements for the nf-core umi_tools module"
+
 # Install apt packages
 RUN apt-get update \
  && apt-get install -y --no-install-recommends \
  procps=2:3.3.15-2 \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*
+
 # Install conda packages
 COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nfcore-umitools-0.1/bin:$PATH
+RUN conda env create -f /environment.yml && conda clean -a

tools/umi_tools/dedup/main.nf

@@ -3,14 +3,6 @@
 // Specify DSL2
 nextflow.preview.dsl = 2
 
-// Include NfUtils
-params.internal_classpath = "umi_tools/groovy/NfUtils.groovy"
-Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(new File(params.internal_classpath));
-GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance();
-
-// Define internal params
-module_name = 'dedup'
-
 // Local default params
 params.internal_outdir = 'results'
 params.internal_process_name = 'dedup'
@@ -212,6 +204,8 @@ process dedup {
     publishDir "umi_tools/dedup/${params.internal_outdir}/${params.internal_process_name}",
         mode: "copy", overwrite: true
 
+    container 'luslab/nf-modules-umitools:latest'
+
     input:
       tuple val(sample_id), path(bai), path(bam)
        

tools/umi_tools/environment.yml

@@ -1,17 +1,13 @@
 # This file creates a conda environment for the umi_tools module
 #   conda env create -f environment.yml
-name: nfcore-umitools-0.1
+name: nfcore-module-umitools
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
   ## basic packages
-  - pigz=2.3.4
+  #- pigz=2.3.4
 
   ## bioconda packages, see above
-  - umi_tools=1.0.1
-
-
-
-  
+  - umi_tools=1.0.1

tools/umi_tools/groovy/NfUtils.groovy

@@ -1,19 +0,0 @@
-class NfUtils{
-    def check_internal_overrides(String moduleName, Map params)
-    {
-        // get params set of keys
-        Set paramsKeySet = params.keySet()
-
-        // Interate through and set internals to the correct parameter at runtime
-        paramsKeySet.each {
-            if(it.startsWith("internal_")) {
-
-                def searchString = moduleName + '_' + it.replace('internal_', '');
-
-                if(paramsKeySet.contains(searchString)) {
-                    params.replace(it, params.get(searchString))
-                }
-            }
-        }
-    }
-}