Merge pull request #1248 from MatthiasZepper/ExtraArgsConsolidation

Improved ext.args consolidation for STAR and TRIMGALORE

CHANGELOG.md

@@ -56,6 +56,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1245](https://github.com/nf-core/rnaseq/pull/1245) - nf test quantify rsem
 - [PR #1246](https://github.com/nf-core/rnaseq/pull/1246) - nf-test quantify pseudoalignment
 - [PR #1247](https://github.com/nf-core/rnaseq/pull/1247) - nf-test prepare_genome
+- [PR #1248](https://github.com/nf-core/rnaseq/pull/1248) - Improved ext.args consolidation for STAR and TRIMGALORE extra_args parameters
 - [PR #1249](https://github.com/nf-core/rnaseq/pull/1249) - Include nf-tests for rsem_merge_counts module
 - [PR #1250](https://github.com/nf-core/rnaseq/pull/1250) - Remove all tags.yml files because the testing system has changed
 - [PR #1251](https://github.com/nf-core/rnaseq/pull/1251) - Replace deseq2qc paths

subworkflows/local/align_star/nextflow.config

@@ -1,20 +1,37 @@
 if (!params.skip_alignment && params.aligner == 'star_salmon') {
     process {
         withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
-            ext.args   = { [
-                '--quantMode TranscriptomeSAM',
-                '--twopassMode Basic',
-                '--outSAMtype BAM Unsorted',
-                '--readFilesCommand zcat',
-                '--runRNGseed 0',
-                '--outFilterMultimapNmax 20',
-                '--alignSJDBoverhangMin 1',
-                '--outSAMattributes NH HI AS NM MD',
-                '--quantTranscriptomeBan Singleend',
-                '--outSAMstrandField intronMotif',
-                params.save_unaligned ? '--outReadsUnmapped Fastx' : '',
-                params.extra_star_align_args ? params.extra_star_align_args.split("\\s(?=--)") : ''
-            ].flatten().unique(false).join(' ').trim() }
+            ext.args   = {
+                    // Function to convert argument strings into a map
+                    def argsToMap = { String args ->
+                        args.split("\\s(?=--)").collectEntries {
+                            def parts = it.trim().split(/\s+/, 2)
+                            [(parts.first()): parts.last()]
+                        }
+                    }
+
+                    // Initialize the map with preconfigured values
+                    def preset_args_map = argsToMap("""
+                        --quantMode TranscriptomeSAM
+                        --twopassMode Basic
+                        --outSAMtype BAM Unsorted
+                        --readFilesCommand zcat
+                        --runRNGseed 0
+                        --outFilterMultimapNmax 20
+                        --alignSJDBoverhangMin 1
+                        --outSAMattributes NH HI AS NM MD
+                        --quantTranscriptomeBan Singleend
+                        --outSAMstrandField intronMotif
+                        ${params.save_unaligned ? '--outReadsUnmapped Fastx' : ''}
+                    """.trim())
+
+                    // Consolidate the extra arguments
+                    def final_args_map = preset_args_map + (params.extra_star_align_args ? argsToMap(params.extra_star_align_args) : [:])
+
+                    // Convert the map back to a list and then to a single string
+                    final_args_map.collect { key, value -> "${key} ${value}" }.join(' ').trim()
+            }
+
             publishDir = [
                 [
                     path: { "${params.outdir}/${params.aligner}/log" },