diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index b676150dd..86960b2e1 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -36,11 +36,10 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') { generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeSAMoutput BanSingleEnd') } } - withName: 'ALIGN_STAR:STAR_ALIGN_IGENOMES' { + 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' {