luslab-umitools | Renamed params and changed relative paths

tools/umi_tools/dedup/main.nf

@@ -1,25 +1,26 @@
 #!/usr/bin/env nextflow
 
 // Include NfUtils
+params.classpath = "umi_tools/groovy/NfUtils.groovy"
 Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(new File(params.classpath));
 GroovyObject nfUtils = (GroovyObject) groovyClass.newInstance();
 
 // Define internal params
-module_name = 'umitools'
+module_name = 'dedup'
 
 // Specify DSL2
 nextflow.preview.dsl = 2
 
 // Local default params
-params.internal_outdir = params.outdir
-params.internal_process_name = 'umitools'
+params.internal_outdir = 'results'
+params.internal_process_name = 'dedup'
 
 // Check for internal parameter overrides
 nfUtils.check_internal_overrides(module_name, params)
 
 // dedup reusable component
-process umi_tools {
-    publishDir "${params.internal_outdir}/${params.internal_process_name}",
+process dedup {
+    publishDir "umi_tools/dedup/${params.internal_outdir}/${params.internal_process_name}",
         mode: "copy", overwrite: true
 
     input:

tools/umi_tools/dedup/test/test.nf

@@ -4,12 +4,12 @@
 nextflow.preview.dsl=2
 
 // Log
-log.info ("Starting test pipeline for BAM deduplication")
+log.info ("Starting test for BAM deduplication")
 
 /* Module inclusions 
 --------------------------------------------------------------------------------------*/
 
-include umi_tools from './umi-tools.nf'
+include dedup from '../main.nf'
 
 /*------------------------------------------------------------------------------------*/
 /* Define input channels
@@ -52,8 +52,8 @@ Channel
 workflow {
 
     // Run dedup
-    umi_tools( ch_test_meta_bambai )
+    dedup ( ch_test_meta_bambai )
 
     // Collect file names and view output
-    umi_tools.out.dedupBam | view
+    dedup.out.dedupBam | view
 }