Remove method from config, tidy up

Author: pinin4fjords

workflows/rnaseq/nextflow.config

@@ -21,31 +21,6 @@ includeConfig "../../subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextf
 includeConfig "../../subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config"
 includeConfig "../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/nextflow.config"
 
-def umi_dedup_args() {
-    if (params.umi_dedup_tool == "umicollapse") {
-        def algo = params.umitools_grouping_method
-        if (params.umitools_grouping_method == 'directional') {
-            algo = 'dir'
-        } else if (params.umitools_grouping_method == 'adjacency') {
-            algo = 'adj'
-        } else if (params.umitools_grouping_method == 'cluster') {
-            algo = 'cc'
-        }
-        return { [
-            '--two-pass',
-            meta.single_end                 ? '' : '--paired --remove-unpaired --remove-chimeric',
-            params.umitools_grouping_method ? "--algo '${algo}'" : '',
-            params.umitools_umi_separator   ? "--umi-sep '${params.umitools_umi_separator}'" : ''
-        ].join(' ').trim() }
-    } else {
-        return { [
-            meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
-            params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
-            params.umitools_umi_separator   ? "--umi-separator='${params.umitools_umi_separator}'" : ''
-        ].join(' ').trim() }
-    }
-}
-
 //
 // STAR Salmon alignment options
 //
@@ -160,7 +135,6 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
             }
 
             withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMI(COLLAPSE|TOOLS)_TRANSCRIPTOME:UMI(COLLAPSE|TOOLS_DEDUP)' {
-                ext.args = umi_dedup_args()
                 ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted" }
                 publishDir = [
                     [
@@ -249,8 +223,25 @@ if (!params.skip_alignment) {
 
     if (params.with_umi && ['star_salmon','hisat2'].contains(params.aligner)) {
         process {
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_(GEN|TRANSCRIPT)OME:UMITOOLS_DEDUP' {
+                ext.args = { [
+                    meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
+                    params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
+                    params.umitools_umi_separator   ? "--umi-separator='${params.umitools_umi_separator}'" : ''
+                ].join(' ').trim() }
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_(GEN|TRANSCRIPT)OME:UMICOLLAPSE' {
+                ext.args = { [
+                    '--two-pass',
+                    meta.single_end                 ? '' : '--paired --remove-unpaired --remove-chimeric',
+                    params.umitools_grouping_method ? "--algo '" + ['directional':'dir','adjacency':'adj','cluster':'cc'].get(params.umitools_grouping_method, '') + "'" : '',
+                    params.umitools_umi_separator   ? "--umi-sep '${params.umitools_umi_separator}'" : '',
+                ].join(' ').trim()}
+            }
+
             withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMI(COLLAPSE|TOOLS)_GENOME:UMI(COLLAPSE|TOOLS_DEDUP)' {
-                ext.args = umi_dedup_args()
                 ext.prefix = { "${meta.id}.umi_dedup.sorted" }
                 publishDir = [
                     [