Refine config setup

pinin4fjords · pinin4fjords · commit 4f8de9450eaa · 2024-10-22T22:17:41.000+01:00
diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config
@@ -33,12 +33,20 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
 
         withName: '.*:ALIGN_STAR:STAR_ALIGN' {
             ext.args   = {
-                    generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeSAMoutput BanSingleEnd')
+                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')
+                generateStarAlignArgs(
+                    params.save_unaligned,
+                    params.contaminant_screening,
+                    (params.extra_star_align_args ?: '') + ' --quantTranscriptomeBan Singleend'
+                )
             }
         }
         withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {

Original file line number	Diff line number	Diff line change
`@@ -33,12 +33,20 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {`
`33`	`33`
`34`	`34`	`withName: '.*:ALIGN_STAR:STAR_ALIGN' {`
`35`	`35`	`ext.args = {`
`36`		`- generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeSAMoutput BanSingleEnd')`
	`36`	`+ generateStarAlignArgs(`
	`37`	`+ params.save_unaligned,`
	`38`	`+ params.contaminant_screening,`
	`39`	`+ (params.extra_star_align_args ?: '') + ' --quantTranscriptomeSAMoutput BanSingleEnd'`
	`40`	`+ )`
`37`	`41`	`}`
`38`	`42`	`}`
`39`	`43`	`withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {`
`40`	`44`	`ext.args = {`
`41`		`- generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeBan Singleend')`
	`45`	`+ generateStarAlignArgs(`
	`46`	`+ params.save_unaligned,`
	`47`	`+ params.contaminant_screening,`
	`48`	`+ (params.extra_star_align_args ?: '') + ' --quantTranscriptomeBan Singleend'`
	`49`	`+ )`
`42`	`50`	`}`
`43`	`51`	`}`
`44`	`52`	`withName: '.:ALIGN_STAR:STAR_ALIGN\|.:ALIGN_STAR:STAR_ALIGN_IGENOMES' {`