Fix argument conflict between STAR versions

Author: pinin4fjords

subworkflows/local/align_star/nextflow.config

@@ -1,36 +1,48 @@
+def generateStarAlignArgs(save_unaligned, contaminant_screening, extra_star_align_args) {
+    def argsToMap = { String args ->
+        args.split(/\s(?=--)/).collectEntries {
+            def parts = it.trim().split(/\s+/, 2)
+            [(parts[0]): parts.size() > 1 ? parts[1] : '']
+        }
+    }
+
+    def base_args = """
+        --quantMode TranscriptomeSAM
+        --twopassMode Basic
+        --outSAMtype BAM Unsorted
+        --readFilesCommand zcat
+        --runRNGseed 0
+        --outFilterMultimapNmax 20
+        --alignSJDBoverhangMin 1
+        --outSAMattributes NH HI AS NM MD
+        --outSAMstrandField intronMotif
+    """.trim()
+
+    if (save_unaligned || contaminant_screening) {
+        base_args += "\n--outReadsUnmapped Fastx"
+    }
+
+    def final_args_map = argsToMap(base_args) + (extra_star_align_args ? argsToMap(extra_star_align_args) : [:])
+    final_args_map.collect { key, value -> "${key} ${value}".trim() }.join(' ')
+}
+
 if (!params.skip_alignment && params.aligner == 'star_salmon') {
     process {
-        withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
-            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
-                        --quantTranscriptomeSAMoutput BanSingleEnd
-                        --outSAMstrandField intronMotif
-                        ${params.save_unaligned || params.contaminant_screening ? '--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) : [:])
+        // We have to condition this, because the args are slightly different between the latest STAR and the one compatible with iGenomes
 
-                    // Convert the map back to a list and then to a single string
-                    final_args_map.collect { key, value -> "${key} ${value}" }.join(' ').trim()
+        withName: '.*:ALIGN_STAR:STAR_ALIGN' {
+            ext.args   = {
+                    generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeSAMoutput BanSingleEnd')
+            }
+        }
+        withName: 'ALIGN_STAR:STAR_ALIGN_IGENOMES' {
+            ext.args   = {
+                    generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeBan Singleend')
             }
+        
+        }
+        withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
 
             publishDir = [
                 [